bool update_forcefield(FILE *fplog,
int nfile,t_filenm fnm[],t_forcerec *fr,
int natoms,rvec x[],matrix box)
{
static int ntry,ntried;
int i,j;
bool bDone;
/* First time around we have to read the parameters */
if (nparm == 0) {
range = read_range(ftp2fn(efDAT,nfile,fnm),&nparm);
if (nparm == 0)
gmx_fatal(FARGS,"No correct parameter info in %s",ftp2fn(efDAT,nfile,fnm));
snew(param_val,nparm);
if (opt2bSet("-ga",nfile,fnm)) {
/* Genetic algorithm time */
ga = init_ga(fplog,opt2fn("-ga",nfile,fnm),nparm,range);
}
else {
/* Determine the grid size */
ntry = 1;
for(i=0; (i<nparm); i++)
ntry *= range[i].np;
ntried = 0;
fprintf(fplog,"Going to try %d different combinations of %d parameters\n",
ntry,nparm);
}
}
if (ga) {
update_ga(fplog,range,ga);
}
else {
/* Increment the counter
* Non-trivial, since this is nparm nested loops in principle
*/
for(i=0; (i<nparm); i++) {
if (param_val[i] < (range[i].np-1)) {
param_val[i]++;
for(j=0; (j<i); j++)
param_val[j] = 0;
ntried++;
break;
}
}
if (i == nparm) {
fprintf(fplog,"Finished with %d out of %d iterations\n",ntried+1,ntry);
return TRUE;
}
}
/* Now do the real updating */
update_ff(fr,nparm,range,param_val);
/* Update box and coordinates if necessary */
scale_box(natoms,x,box);
return FALSE;
}
int cmain(int argc,char *argv[])
{
int step,natoms;
real t,lambda;
t_inputrec ir;
t_topology top;
matrix box;
rvec *x,*v,*f;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efXML, "-r", NULL, ffREAD },
{ efXML, "-o", NULL, ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,0,NFILE,fnm,0,NULL,0,NULL,0,NULL);
init_top(&top);
if (opt2bSet("-r",NFILE,fnm))
read_xml(opt2fn("-r",NFILE,fnm),&step,&t,&lambda,&ir,
box,&natoms,&x,&v,&f,&top);
else {
t_tpxheader tpx;
read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&tpx,FALSE);
snew(x,tpx.natoms);
snew(v,tpx.natoms);
f = NULL;
read_tpx(ftp2fn(efTPX,NFILE,fnm),&step,&t,&lambda,&ir,
box,&natoms,x,v,f,&top);
}
/*write_xml(opt2fn("-o",NFILE,fnm),step,t,lambda,&ir,box,natoms,x,v,f,&top);*/
return 0;
}
int gmx_rmsf(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the root mean square fluctuation (RMSF, i.e. standard ",
"deviation) of atomic positions in the trajectory (supplied with [TT]-f[tt])",
"after (optionally) fitting to a reference frame (supplied with [TT]-s[tt]).[PAR]",
"With option [TT]-oq[tt] the RMSF values are converted to B-factor",
"values, which are written to a [REF].pdb[ref] file with the coordinates, of the",
"structure file, or of a [REF].pdb[ref] file when [TT]-q[tt] is specified.",
"Option [TT]-ox[tt] writes the B-factors to a file with the average",
"coordinates.[PAR]",
"With the option [TT]-od[tt] the root mean square deviation with",
"respect to the reference structure is calculated.[PAR]",
"With the option [TT]-aniso[tt], [THISMODULE] will compute anisotropic",
"temperature factors and then it will also output average coordinates",
"and a [REF].pdb[ref] file with ANISOU records (corresonding to the [TT]-oq[tt]",
"or [TT]-ox[tt] option). Please note that the U values",
"are orientation-dependent, so before comparison with experimental data",
"you should verify that you fit to the experimental coordinates.[PAR]",
"When a [REF].pdb[ref] input file is passed to the program and the [TT]-aniso[tt]",
"flag is set",
"a correlation plot of the Uij will be created, if any anisotropic",
"temperature factors are present in the [REF].pdb[ref] file.[PAR]",
"With option [TT]-dir[tt] the average MSF (3x3) matrix is diagonalized.",
"This shows the directions in which the atoms fluctuate the most and",
"the least."
};
static gmx_bool bRes = FALSE, bAniso = FALSE, bFit = TRUE;
t_pargs pargs[] = {
{ "-res", FALSE, etBOOL, {&bRes},
"Calculate averages for each residue" },
{ "-aniso", FALSE, etBOOL, {&bAniso},
"Compute anisotropic termperature factors" },
{ "-fit", FALSE, etBOOL, {&bFit},
"Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match." }
};
int natom;
int i, m, teller = 0;
real t, *w_rls;
t_topology top;
int ePBC;
t_atoms *pdbatoms, *refatoms;
matrix box, pdbbox;
rvec *x, *pdbx, *xref;
t_trxstatus *status;
const char *label;
FILE *fp; /* the graphics file */
const char *devfn, *dirfn;
int resind;
gmx_bool bReadPDB;
int *index;
int isize;
char *grpnames;
real bfac, pdb_bfac, *Uaver;
double **U, *xav;
int aid;
rvec *rmsd_x = nullptr;
double *rmsf, invcount, totmass;
int d;
real count = 0;
rvec xcm;
gmx_rmpbc_t gpbc = nullptr;
gmx_output_env_t *oenv;
const char *leg[2] = { "MD", "X-Ray" };
t_filenm fnm[] = {
{ efTRX, "-f", nullptr, ffREAD },
{ efTPS, nullptr, nullptr, ffREAD },
{ efNDX, nullptr, nullptr, ffOPTRD },
{ efPDB, "-q", nullptr, ffOPTRD },
{ efPDB, "-oq", "bfac", ffOPTWR },
{ efPDB, "-ox", "xaver", ffOPTWR },
{ efXVG, "-o", "rmsf", ffWRITE },
{ efXVG, "-od", "rmsdev", ffOPTWR },
{ efXVG, "-oc", "correl", ffOPTWR },
{ efLOG, "-dir", "rmsf", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, nullptr,
&oenv))
{
return 0;
}
bReadPDB = ftp2bSet(efPDB, NFILE, fnm);
devfn = opt2fn_null("-od", NFILE, fnm);
dirfn = opt2fn_null("-dir", NFILE, fnm);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xref, nullptr, box, TRUE);
const char *title = *top.name;
snew(w_rls, top.atoms.nr);
fprintf(stderr, "Select group(s) for root mean square calculation\n");
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpnames);
/* Set the weight */
for (i = 0; i < isize; i++)
{
w_rls[index[i]] = top.atoms.atom[index[i]].m;
}
/* Malloc the rmsf arrays */
snew(xav, isize*DIM);
snew(U, isize);
for (i = 0; i < isize; i++)
{
snew(U[i], DIM*DIM);
}
snew(rmsf, isize);
if (devfn)
{
snew(rmsd_x, isize);
}
if (bReadPDB)
{
t_topology *top_pdb;
snew(top_pdb, 1);
/* Read coordinates twice */
read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, nullptr, nullptr, nullptr, pdbbox, FALSE);
snew(pdbatoms, 1);
*pdbatoms = top_pdb->atoms;
read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, nullptr, &pdbx, nullptr, pdbbox, FALSE);
/* TODO Should this assert that top_pdb->atoms.nr == top.atoms.nr?
* See discussion at https://gerrit.gromacs.org/#/c/6430/1 */
title = *top_pdb->name;
snew(refatoms, 1);
*refatoms = top_pdb->atoms;
sfree(top_pdb);
}
else
{
pdbatoms = &top.atoms;
refatoms = &top.atoms;
pdbx = xref;
snew(pdbatoms->pdbinfo, pdbatoms->nr);
pdbatoms->havePdbInfo = TRUE;
copy_mat(box, pdbbox);
}
if (bFit)
{
sub_xcm(xref, isize, index, top.atoms.atom, xcm, FALSE);
}
natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
if (bFit)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natom);
}
/* Now read the trj again to compute fluctuations */
teller = 0;
do
{
if (bFit)
{
/* Remove periodic boundary */
gmx_rmpbc(gpbc, natom, box, x);
/* Set center of mass to zero */
sub_xcm(x, isize, index, top.atoms.atom, xcm, FALSE);
/* Fit to reference structure */
do_fit(natom, w_rls, xref, x);
}
/* Calculate Anisotropic U Tensor */
for (i = 0; i < isize; i++)
{
aid = index[i];
for (d = 0; d < DIM; d++)
{
xav[i*DIM + d] += x[aid][d];
for (m = 0; m < DIM; m++)
{
U[i][d*DIM + m] += x[aid][d]*x[aid][m];
}
}
}
if (devfn)
{
/* Calculate RMS Deviation */
for (i = 0; (i < isize); i++)
{
aid = index[i];
for (d = 0; (d < DIM); d++)
{
rmsd_x[i][d] += gmx::square(x[aid][d]-xref[aid][d]);
}
}
}
count += 1.0;
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
close_trx(status);
if (bFit)
{
gmx_rmpbc_done(gpbc);
}
invcount = 1.0/count;
snew(Uaver, DIM*DIM);
totmass = 0;
for (i = 0; i < isize; i++)
{
for (d = 0; d < DIM; d++)
{
xav[i*DIM + d] *= invcount;
}
for (d = 0; d < DIM; d++)
{
for (m = 0; m < DIM; m++)
{
U[i][d*DIM + m] = U[i][d*DIM + m]*invcount
- xav[i*DIM + d]*xav[i*DIM + m];
Uaver[3*d+m] += top.atoms.atom[index[i]].m*U[i][d*DIM + m];
}
}
totmass += top.atoms.atom[index[i]].m;
}
for (d = 0; d < DIM*DIM; d++)
{
Uaver[d] /= totmass;
}
if (bRes)
{
for (d = 0; d < DIM*DIM; d++)
{
average_residues(nullptr, U, d, isize, index, w_rls, &top.atoms);
}
}
if (bAniso)
{
for (i = 0; i < isize; i++)
{
aid = index[i];
pdbatoms->pdbinfo[aid].bAnisotropic = TRUE;
pdbatoms->pdbinfo[aid].uij[U11] = static_cast<int>(1e6*U[i][XX*DIM + XX]);
pdbatoms->pdbinfo[aid].uij[U22] = static_cast<int>(1e6*U[i][YY*DIM + YY]);
pdbatoms->pdbinfo[aid].uij[U33] = static_cast<int>(1e6*U[i][ZZ*DIM + ZZ]);
pdbatoms->pdbinfo[aid].uij[U12] = static_cast<int>(1e6*U[i][XX*DIM + YY]);
pdbatoms->pdbinfo[aid].uij[U13] = static_cast<int>(1e6*U[i][XX*DIM + ZZ]);
pdbatoms->pdbinfo[aid].uij[U23] = static_cast<int>(1e6*U[i][YY*DIM + ZZ]);
}
}
if (bRes)
{
label = "Residue";
}
else
{
label = "Atom";
}
for (i = 0; i < isize; i++)
{
rmsf[i] = U[i][XX*DIM + XX] + U[i][YY*DIM + YY] + U[i][ZZ*DIM + ZZ];
}
if (dirfn)
{
fprintf(stdout, "\n");
print_dir(stdout, Uaver);
fp = gmx_ffopen(dirfn, "w");
print_dir(fp, Uaver);
gmx_ffclose(fp);
}
for (i = 0; i < isize; i++)
{
sfree(U[i]);
}
sfree(U);
/* Write RMSF output */
if (bReadPDB)
{
bfac = 8.0*M_PI*M_PI/3.0*100;
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "B-Factors",
label, "(A\\b\\S\\So\\N\\S2\\N)", oenv);
xvgr_legend(fp, 2, leg, oenv);
for (i = 0; (i < isize); i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
resind = top.atoms.atom[index[i]].resind;
pdb_bfac = find_pdb_bfac(pdbatoms, &top.atoms.resinfo[resind],
*(top.atoms.atomname[index[i]]));
fprintf(fp, "%5d %10.5f %10.5f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, rmsf[i]*bfac,
pdb_bfac);
}
}
xvgrclose(fp);
}
else
{
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "RMS fluctuation", label, "(nm)", oenv);
for (i = 0; i < isize; i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
fprintf(fp, "%5d %8.4f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, std::sqrt(rmsf[i]));
}
}
xvgrclose(fp);
}
for (i = 0; i < isize; i++)
{
pdbatoms->pdbinfo[index[i]].bfac = 800*M_PI*M_PI/3.0*rmsf[i];
}
if (devfn)
{
for (i = 0; i < isize; i++)
{
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
}
if (bRes)
{
average_residues(rmsf, nullptr, 0, isize, index, w_rls, &top.atoms);
}
/* Write RMSD output */
fp = xvgropen(devfn, "RMS Deviation", label, "(nm)", oenv);
for (i = 0; i < isize; i++)
{
if (!bRes || i+1 == isize ||
top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
{
fprintf(fp, "%5d %8.4f\n",
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, std::sqrt(rmsf[i]));
}
}
xvgrclose(fp);
}
if (opt2bSet("-oq", NFILE, fnm))
{
/* Write a .pdb file with B-factors and optionally anisou records */
for (i = 0; i < isize; i++)
{
rvec_inc(pdbx[index[i]], xcm);
}
write_sto_conf_indexed(opt2fn("-oq", NFILE, fnm), title, pdbatoms, pdbx,
nullptr, ePBC, pdbbox, isize, index);
}
if (opt2bSet("-ox", NFILE, fnm))
{
rvec *bFactorX;
snew(bFactorX, top.atoms.nr);
for (i = 0; i < isize; i++)
{
for (d = 0; d < DIM; d++)
{
bFactorX[index[i]][d] = xcm[d] + xav[i*DIM + d];
}
}
/* Write a .pdb file with B-factors and optionally anisou records */
write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, nullptr,
ePBC, pdbbox, isize, index);
sfree(bFactorX);
}
if (bAniso)
{
correlate_aniso(opt2fn("-oc", NFILE, fnm), refatoms, pdbatoms, oenv);
do_view(oenv, opt2fn("-oc", NFILE, fnm), "-nxy");
}
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
if (devfn)
{
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
}
return 0;
}
int gmx_genion(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] randomly replaces solvent molecules with monoatomic ions.",
"The group of solvent molecules should be continuous and all molecules",
"should have the same number of atoms.",
"The user should add the ion molecules to the topology file or use",
"the [TT]-p[tt] option to automatically modify the topology.[PAR]",
"The ion molecule type, residue and atom names in all force fields",
"are the capitalized element names without sign. This molecule name",
"should be given with [TT]-pname[tt] or [TT]-nname[tt], and the",
"[TT][molecules][tt] section of your topology updated accordingly,",
"either by hand or with [TT]-p[tt]. Do not use an atom name instead!",
"[PAR]Ions which can have multiple charge states get the multiplicity",
"added, without sign, for the uncommon states only.[PAR]",
"For larger ions, e.g. sulfate we recommended using [gmx-insert-molecules]."
};
const char *bugs[] = {
"If you specify a salt concentration existing ions are not taken into "
"account. In effect you therefore specify the amount of salt to be added.",
};
static int p_num = 0, n_num = 0, p_q = 1, n_q = -1;
static const char *p_name = "NA", *n_name = "CL";
static real rmin = 0.6, conc = 0;
static int seed = 1993;
static gmx_bool bNeutral = FALSE;
static t_pargs pa[] = {
{ "-np", FALSE, etINT, {&p_num}, "Number of positive ions" },
{ "-pname", FALSE, etSTR, {&p_name}, "Name of the positive ion" },
{ "-pq", FALSE, etINT, {&p_q}, "Charge of the positive ion" },
{ "-nn", FALSE, etINT, {&n_num}, "Number of negative ions" },
{ "-nname", FALSE, etSTR, {&n_name}, "Name of the negative ion" },
{ "-nq", FALSE, etINT, {&n_q}, "Charge of the negative ion" },
{ "-rmin", FALSE, etREAL, {&rmin}, "Minimum distance between ions" },
{ "-seed", FALSE, etINT, {&seed}, "Seed for random number generator" },
{ "-conc", FALSE, etREAL, {&conc},
"Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [REF].tpr[ref] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
{ "-neutral", FALSE, etBOOL, {&bNeutral}, "This option will add enough ions to neutralize the system. These ions are added on top of those specified with [TT]-np[tt]/[TT]-nn[tt] or [TT]-conc[tt]. "}
};
t_topology top;
rvec *x, *v;
real vol, qtot;
matrix box;
t_atoms atoms;
t_pbc pbc;
int *repl, ePBC;
atom_id *index;
char *grpname;
gmx_bool *bSet;
int i, nw, nwa, nsa, nsalt, iqtot;
gmx_output_env_t *oenv;
gmx_rng_t rng;
t_filenm fnm[] = {
{ efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTO, "-o", NULL, ffWRITE },
{ efTOP, "-p", "topol", ffOPTRW }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
/* Check input for something sensible */
if ((p_num < 0) || (n_num < 0))
{
gmx_fatal(FARGS, "Negative number of ions to add?");
}
if (conc > 0 && (p_num > 0 || n_num > 0))
{
fprintf(stderr, "WARNING: -conc specified, overriding -nn and -np.\n");
}
/* Read atom positions and charges */
read_tps_conf(ftp2fn(efTPR, NFILE, fnm), &top, &ePBC, &x, &v, box, FALSE);
atoms = top.atoms;
/* Compute total charge */
qtot = 0;
for (i = 0; (i < atoms.nr); i++)
{
qtot += atoms.atom[i].q;
}
iqtot = std::round(qtot);
if (conc > 0)
{
/* Compute number of ions to be added */
vol = det(box);
nsalt = std::round(conc*vol*AVOGADRO/1e24);
p_num = abs(nsalt*n_q);
n_num = abs(nsalt*p_q);
}
if (bNeutral)
{
int qdelta = p_num*p_q + n_num*n_q + iqtot;
/* Check if the system is neutralizable
* is (qdelta == p_q*p_num + n_q*n_num) solvable for p_num and n_num? */
int gcd = gmx_greatest_common_divisor(n_q, p_q);
if ((qdelta % gcd) != 0)
{
gmx_fatal(FARGS, "Can't neutralize this system using -nq %d and"
" -pq %d.\n", n_q, p_q);
}
while (qdelta != 0)
{
while (qdelta < 0)
{
p_num++;
qdelta += p_q;
}
while (qdelta > 0)
{
n_num++;
qdelta += n_q;
}
}
}
if ((p_num == 0) && (n_num == 0))
{
fprintf(stderr, "No ions to add, will just copy input configuration.\n");
}
else
{
printf("Will try to add %d %s ions and %d %s ions.\n",
p_num, p_name, n_num, n_name);
printf("Select a continuous group of solvent molecules\n");
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nwa, &index, &grpname);
for (i = 1; i < nwa; i++)
{
if (index[i] != index[i-1]+1)
{
gmx_fatal(FARGS, "The solvent group %s is not continuous: "
"index[%d]=%d, index[%d]=%d",
grpname, i, index[i-1]+1, i+1, index[i]+1);
}
}
nsa = 1;
while ((nsa < nwa) &&
(atoms.atom[index[nsa]].resind ==
atoms.atom[index[nsa-1]].resind))
{
nsa++;
}
if (nwa % nsa)
{
gmx_fatal(FARGS, "Your solvent group size (%d) is not a multiple of %d",
nwa, nsa);
}
nw = nwa/nsa;
fprintf(stderr, "Number of (%d-atomic) solvent molecules: %d\n", nsa, nw);
if (p_num+n_num > nw)
{
gmx_fatal(FARGS, "Not enough solvent for adding ions");
}
if (opt2bSet("-p", NFILE, fnm))
{
update_topol(opt2fn("-p", NFILE, fnm), p_num, n_num, p_name, n_name, grpname);
}
snew(bSet, nw);
snew(repl, nw);
snew(v, atoms.nr);
snew(atoms.pdbinfo, atoms.nr);
set_pbc(&pbc, ePBC, box);
if (seed == 0)
{
rng = gmx_rng_init(gmx_rng_make_seed());
}
else
{
rng = gmx_rng_init(seed);
}
/* Now loop over the ions that have to be placed */
while (p_num-- > 0)
{
insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
1, p_q, p_name, &atoms, rmin, rng);
}
while (n_num-- > 0)
{
insert_ion(nsa, &nw, bSet, repl, index, x, &pbc,
-1, n_q, n_name, &atoms, rmin, rng);
}
gmx_rng_destroy(rng);
fprintf(stderr, "\n");
if (nw)
{
sort_ions(nsa, nw, repl, index, &atoms, x, p_name, n_name);
}
sfree(atoms.pdbinfo);
atoms.pdbinfo = NULL;
}
write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *top.name, &atoms, x, NULL, ePBC, box);
return 0;
}
int gmx_pme_error(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_pme_error[tt] estimates the error of the electrostatic forces",
"if using the sPME algorithm. The flag [TT]-tune[tt] will determine",
"the splitting parameter such that the error is equally",
"distributed over the real and reciprocal space part.",
"The part of the error that stems from self interaction of the particles "
"is computationally demanding. However, a good a approximation is to",
"just use a fraction of the particles for this term which can be",
"indicated by the flag [TT]-self[tt].[PAR]",
};
real fs=0.0; /* 0 indicates: not set by the user */
real user_beta=-1.0;
real fracself=1.0;
t_inputinfo info;
t_state state; /* The state from the tpr input file */
gmx_mtop_t mtop; /* The topology from the tpr input file */
t_inputrec *ir=NULL; /* The inputrec from the tpr file */
FILE *fp=NULL;
t_commrec *cr;
unsigned long PCA_Flags;
gmx_bool bTUNE=FALSE;
gmx_bool bVerbose=FALSE;
int seed=0;
static t_filenm fnm[] = {
{ efTPX, "-s", NULL, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
{ efTPX, "-so", "tuned", ffOPTWR }
};
output_env_t oenv=NULL;
t_pargs pa[] = {
{ "-beta", FALSE, etREAL, {&user_beta},
"If positive, overwrite ewald_beta from [TT].tpr[tt] file with this value" },
{ "-tune", FALSE, etBOOL, {&bTUNE},
"Tune the splitting parameter such that the error is equally distributed between real and reciprocal space" },
{ "-self", FALSE, etREAL, {&fracself},
"If between 0.0 and 1.0, determine self interaction error from just this fraction of the charged particles" },
{ "-seed", FALSE, etINT, {&seed},
"Random number seed used for Monte Carlo algorithm when [TT]-self[tt] is set to a value between 0.0 and 1.0" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
#ifdef GMX_LIB_MPI
MPI_Barrier(MPI_COMM_WORLD);
#endif
if (MASTER(cr))
CopyRight(stderr,argv[0]);
PCA_Flags = PCA_NOEXIT_ON_ARGS;
PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
parse_common_args(&argc,argv,PCA_Flags,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL,&oenv);
if (!bTUNE)
bTUNE = opt2bSet("-so",NFILE,fnm);
info.n_entries = 1;
/* Allocate memory for the inputinfo struct: */
create_info(&info);
info.fourier_sp[0] = fs;
/* Read in the tpr file and open logfile for reading */
if (MASTER(cr))
{
snew(ir,1);
read_tpr_file(opt2fn("-s",NFILE,fnm), &info, &state, &mtop, ir, user_beta,fracself);
fp=fopen(opt2fn("-o",NFILE,fnm),"w");
}
/* Check consistency if the user provided fourierspacing */
if (fs > 0 && MASTER(cr))
{
/* Recalculate the grid dimensions using fourierspacing from user input */
info.nkx[0] = 0;
info.nky[0] = 0;
info.nkz[0] = 0;
calc_grid(stdout,state.box,info.fourier_sp[0],&(info.nkx[0]),&(info.nky[0]),&(info.nkz[0]));
if ( (ir->nkx != info.nkx[0]) || (ir->nky != info.nky[0]) || (ir->nkz != info.nkz[0]) )
gmx_fatal(FARGS, "Wrong fourierspacing %f nm, input file grid = %d x %d x %d, computed grid = %d x %d x %d",
fs,ir->nkx,ir->nky,ir->nkz,info.nkx[0],info.nky[0],info.nkz[0]);
}
/* Estimate (S)PME force error */
/* Determine the volume of the simulation box */
if (MASTER(cr))
{
info.volume = det(state.box);
calc_recipbox(state.box,info.recipbox);
info.natoms = mtop.natoms;
info.bTUNE = bTUNE;
}
if (PAR(cr))
bcast_info(&info, cr);
/* Get an error estimate of the input tpr file and do some tuning if requested */
estimate_PME_error(&info, &state, &mtop, fp, bVerbose, seed, cr);
if (MASTER(cr))
{
/* Write out optimized tpr file if requested */
if ( opt2bSet("-so",NFILE,fnm) || bTUNE )
{
ir->ewald_rtol=info.ewald_rtol[0];
write_tpx_state(opt2fn("-so",NFILE,fnm),ir,&state,&mtop);
}
please_cite(fp,"Wang2010");
fclose(fp);
}
if (gmx_parallel_env_initialized())
{
gmx_finalize();
}
return 0;
}
int gmx_polystat(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] plots static properties of polymers as a function of time",
"and prints the average.[PAR]",
"By default it determines the average end-to-end distance and radii",
"of gyration of polymers. It asks for an index group and split this",
"into molecules. The end-to-end distance is then determined using",
"the first and the last atom in the index group for each molecules.",
"For the radius of gyration the total and the three principal components",
"for the average gyration tensor are written.",
"With option [TT]-v[tt] the eigenvectors are written.",
"With option [TT]-pc[tt] also the average eigenvalues of the individual",
"gyration tensors are written.",
"With option [TT]-i[tt] the mean square internal distances are",
"written.[PAR]",
"With option [TT]-p[tt] the persistence length is determined.",
"The chosen index group should consist of atoms that are",
"consecutively bonded in the polymer mainchains.",
"The persistence length is then determined from the cosine of",
"the angles between bonds with an index difference that is even,",
"the odd pairs are not used, because straight polymer backbones",
"are usually all trans and therefore only every second bond aligns.",
"The persistence length is defined as number of bonds where",
"the average cos reaches a value of 1/e. This point is determined",
"by a linear interpolation of [LOG]<cos>[log]."
};
static gmx_bool bMW = TRUE, bPC = FALSE;
t_pargs pa[] = {
{ "-mw", FALSE, etBOOL, {&bMW},
"Use the mass weighting for radii of gyration" },
{ "-pc", FALSE, etBOOL, {&bPC},
"Plot average eigenvalues" }
};
t_filenm fnm[] = {
{ efTPR, nullptr, nullptr, ffREAD },
{ efTRX, "-f", nullptr, ffREAD },
{ efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-o", "polystat", ffWRITE },
{ efXVG, "-v", "polyvec", ffOPTWR },
{ efXVG, "-p", "persist", ffOPTWR },
{ efXVG, "-i", "intdist", ffOPTWR }
};
#define NFILE asize(fnm)
t_topology *top;
gmx_output_env_t *oenv;
int ePBC;
int isize, *index, nmol, *molind, mol, nat_min = 0, nat_max = 0;
char *grpname;
t_trxstatus *status;
real t;
rvec *x, *bond = nullptr;
matrix box;
int natoms, i, j, frame, ind0, ind1, a, d, d2, ord[DIM] = {0};
dvec cm, sum_eig = {0, 0, 0};
double **gyr, **gyr_all, eig[DIM], **eigv;
double sum_eed2, sum_eed2_tot, sum_gyro, sum_gyro_tot, sum_pers_tot;
int *ninp = nullptr;
double *sum_inp = nullptr, pers;
double *intd, ymax, ymin;
double mmol, m;
char title[STRLEN];
FILE *out, *outv, *outp, *outi;
const char *leg[8] = {
"end to end", "<R\\sg\\N>",
"<R\\sg\\N> eig1", "<R\\sg\\N> eig2", "<R\\sg\\N> eig3",
"<R\\sg\\N eig1>", "<R\\sg\\N eig2>", "<R\\sg\\N eig3>"
};
char **legp, buf[STRLEN];
gmx_rmpbc_t gpbc = nullptr;
if (!parse_common_args(&argc, argv,
PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
snew(top, 1);
ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm),
nullptr, box, &natoms, nullptr, nullptr, top);
fprintf(stderr, "Select a group of polymer mainchain atoms:\n");
get_index(&top->atoms, ftp2fn_null(efNDX, NFILE, fnm),
1, &isize, &index, &grpname);
snew(molind, top->mols.nr+1);
nmol = 0;
mol = -1;
for (i = 0; i < isize; i++)
{
if (i == 0 || index[i] >= top->mols.index[mol+1])
{
molind[nmol++] = i;
do
{
mol++;
}
while (index[i] >= top->mols.index[mol+1]);
}
}
molind[nmol] = i;
nat_min = top->atoms.nr;
nat_max = 0;
for (mol = 0; mol < nmol; mol++)
{
nat_min = std::min(nat_min, molind[mol+1]-molind[mol]);
nat_max = std::max(nat_max, molind[mol+1]-molind[mol]);
}
fprintf(stderr, "Group %s consists of %d molecules\n", grpname, nmol);
fprintf(stderr, "Group size per molecule, min: %d atoms, max %d atoms\n",
nat_min, nat_max);
sprintf(title, "Size of %d polymers", nmol);
out = xvgropen(opt2fn("-o", NFILE, fnm), title, output_env_get_xvgr_tlabel(oenv), "(nm)",
oenv);
xvgr_legend(out, bPC ? 8 : 5, leg, oenv);
if (opt2bSet("-v", NFILE, fnm))
{
outv = xvgropen(opt2fn("-v", NFILE, fnm), "Principal components",
output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
snew(legp, DIM*DIM);
for (d = 0; d < DIM; d++)
{
for (d2 = 0; d2 < DIM; d2++)
{
sprintf(buf, "eig%d %c", d+1, 'x'+d2);
legp[d*DIM+d2] = gmx_strdup(buf);
}
}
xvgr_legend(outv, DIM*DIM, (const char**)legp, oenv);
}
else
{
outv = nullptr;
}
if (opt2bSet("-p", NFILE, fnm))
{
outp = xvgropen(opt2fn("-p", NFILE, fnm), "Persistence length",
output_env_get_xvgr_tlabel(oenv), "bonds", oenv);
snew(bond, nat_max-1);
snew(sum_inp, nat_min/2);
snew(ninp, nat_min/2);
}
else
{
outp = nullptr;
}
if (opt2bSet("-i", NFILE, fnm))
{
outi = xvgropen(opt2fn("-i", NFILE, fnm), "Internal distances",
"n", "<R\\S2\\N(n)>/n (nm\\S2\\N)", oenv);
i = index[molind[1]-1] - index[molind[0]]; /* Length of polymer -1 */
snew(intd, i);
}
else
{
intd = nullptr;
outi = nullptr;
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(gyr, DIM);
snew(gyr_all, DIM);
snew(eigv, DIM);
for (d = 0; d < DIM; d++)
{
snew(gyr[d], DIM);
snew(gyr_all[d], DIM);
snew(eigv[d], DIM);
}
frame = 0;
sum_eed2_tot = 0;
sum_gyro_tot = 0;
sum_pers_tot = 0;
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
do
{
gmx_rmpbc(gpbc, natoms, box, x);
sum_eed2 = 0;
for (d = 0; d < DIM; d++)
{
clear_dvec(gyr_all[d]);
}
if (bPC)
{
clear_dvec(sum_eig);
}
if (outp)
{
for (i = 0; i < nat_min/2; i++)
{
sum_inp[i] = 0;
ninp[i] = 0;
}
}
for (mol = 0; mol < nmol; mol++)
{
ind0 = molind[mol];
ind1 = molind[mol+1];
/* Determine end to end distance */
sum_eed2 += distance2(x[index[ind0]], x[index[ind1-1]]);
/* Determine internal distances */
if (outi)
{
calc_int_dist(intd, x, index[ind0], index[ind1-1]);
}
/* Determine the radius of gyration */
clear_dvec(cm);
for (d = 0; d < DIM; d++)
{
clear_dvec(gyr[d]);
}
mmol = 0;
for (i = ind0; i < ind1; i++)
{
a = index[i];
if (bMW)
{
m = top->atoms.atom[a].m;
}
else
{
m = 1;
}
mmol += m;
for (d = 0; d < DIM; d++)
{
cm[d] += m*x[a][d];
for (d2 = 0; d2 < DIM; d2++)
{
gyr[d][d2] += m*x[a][d]*x[a][d2];
}
}
}
dsvmul(1/mmol, cm, cm);
for (d = 0; d < DIM; d++)
{
for (d2 = 0; d2 < DIM; d2++)
{
gyr[d][d2] = gyr[d][d2]/mmol - cm[d]*cm[d2];
gyr_all[d][d2] += gyr[d][d2];
}
}
if (bPC)
{
gyro_eigen(gyr, eig, eigv, ord);
for (d = 0; d < DIM; d++)
{
sum_eig[d] += eig[ord[d]];
}
}
if (outp)
{
for (i = ind0; i < ind1-1; i++)
{
rvec_sub(x[index[i+1]], x[index[i]], bond[i-ind0]);
unitv(bond[i-ind0], bond[i-ind0]);
}
for (i = ind0; i < ind1-1; i++)
{
for (j = 0; (i+j < ind1-1 && j < nat_min/2); j += 2)
{
sum_inp[j] += iprod(bond[i-ind0], bond[i-ind0+j]);
ninp[j]++;
}
}
}
}
sum_eed2 /= nmol;
sum_gyro = 0;
for (d = 0; d < DIM; d++)
{
for (d2 = 0; d2 < DIM; d2++)
{
gyr_all[d][d2] /= nmol;
}
sum_gyro += gyr_all[d][d];
}
gyro_eigen(gyr_all, eig, eigv, ord);
fprintf(out, "%10.3f %8.4f %8.4f %8.4f %8.4f %8.4f",
t*output_env_get_time_factor(oenv),
std::sqrt(sum_eed2), sqrt(sum_gyro),
std::sqrt(eig[ord[0]]), std::sqrt(eig[ord[1]]), std::sqrt(eig[ord[2]]));
if (bPC)
{
for (d = 0; d < DIM; d++)
{
fprintf(out, " %8.4f", std::sqrt(sum_eig[d]/nmol));
}
}
fprintf(out, "\n");
if (outv)
{
fprintf(outv, "%10.3f", t*output_env_get_time_factor(oenv));
for (d = 0; d < DIM; d++)
{
for (d2 = 0; d2 < DIM; d2++)
{
fprintf(outv, " %6.3f", eigv[ord[d]][d2]);
}
}
fprintf(outv, "\n");
}
sum_eed2_tot += sum_eed2;
sum_gyro_tot += sum_gyro;
if (outp)
{
i = -1;
for (j = 0; j < nat_min/2; j += 2)
{
sum_inp[j] /= ninp[j];
if (i == -1 && sum_inp[j] <= std::exp(-1.0))
{
i = j;
}
}
if (i == -1)
{
pers = j;
}
else
{
/* Do linear interpolation on a log scale */
pers = i - 2.0
+ 2.0*(std::log(sum_inp[i-2]) + 1.0)/(std::log(sum_inp[i-2]) - std::log(sum_inp[i]));
}
fprintf(outp, "%10.3f %8.4f\n", t*output_env_get_time_factor(oenv), pers);
sum_pers_tot += pers;
}
frame++;
}
while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
close_trx(status);
xvgrclose(out);
if (outv)
{
xvgrclose(outv);
}
if (outp)
{
xvgrclose(outp);
}
sum_eed2_tot /= frame;
sum_gyro_tot /= frame;
sum_pers_tot /= frame;
fprintf(stdout, "\nAverage end to end distance: %.3f (nm)\n",
std::sqrt(sum_eed2_tot));
fprintf(stdout, "\nAverage radius of gyration: %.3f (nm)\n",
std::sqrt(sum_gyro_tot));
if (opt2bSet("-p", NFILE, fnm))
{
fprintf(stdout, "\nAverage persistence length: %.2f bonds\n",
sum_pers_tot);
}
/* Handle printing of internal distances. */
if (outi)
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(outi, "@ xaxes scale Logarithmic\n");
}
ymax = -1;
ymin = 1e300;
j = index[molind[1]-1] - index[molind[0]]; /* Polymer length -1. */
for (i = 0; i < j; i++)
{
intd[i] /= (i + 1) * frame * nmol;
if (intd[i] > ymax)
{
ymax = intd[i];
}
if (intd[i] < ymin)
{
ymin = intd[i];
}
}
xvgr_world(outi, 1, ymin, j, ymax, oenv);
for (i = 0; i < j; i++)
{
fprintf(outi, "%d %8.4f\n", i+1, intd[i]);
}
xvgrclose(outi);
}
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
if (opt2bSet("-v", NFILE, fnm))
{
do_view(oenv, opt2fn("-v", NFILE, fnm), "-nxy");
}
if (opt2bSet("-p", NFILE, fnm))
{
do_view(oenv, opt2fn("-p", NFILE, fnm), "-nxy");
}
return 0;
}
int gmx_mdmat(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_mdmat[tt] makes distance matrices consisting of the smallest distance",
"between residue pairs. With [TT]-frames[tt], these distance matrices can be",
"stored in order to see differences in tertiary structure as a",
"function of time. If you choose your options unwisely, this may generate",
"a large output file. By default, only an averaged matrix over the whole",
"trajectory is output.",
"Also a count of the number of different atomic contacts between",
"residues over the whole trajectory can be made.",
"The output can be processed with [TT]xpm2ps[tt] to make a PostScript (tm) plot."
};
static real truncate = 1.5;
static gmx_bool bAtom = FALSE;
static int nlevels = 40;
t_pargs pa[] = {
{ "-t", FALSE, etREAL, {&truncate},
"trunc distance" },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Discretize distance in this number of levels" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXPM, "-mean", "dm", ffWRITE },
{ efXPM, "-frames", "dmf", ffOPTWR },
{ efXVG, "-no", "num", ffOPTWR },
};
#define NFILE asize(fnm)
FILE *out = NULL, *fp;
t_topology top;
int ePBC;
t_atoms useatoms;
int isize;
atom_id *index;
char *grpname;
int *rndx, *natm, prevres, newres;
int i, j, nres, natoms, nframes, it, trxnat;
t_trxstatus *status;
int nr0;
gmx_bool bCalcN, bFrames;
real t, ratio;
char title[256], label[234];
t_rgb rlo, rhi;
rvec *x;
real **mdmat, *resnr, **totmdmat;
int **nmat, **totnmat;
real *mean_n;
int *tot_n;
matrix box;
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
fprintf(stderr, "Will truncate at %f nm\n", truncate);
bCalcN = opt2bSet("-no", NFILE, fnm);
bFrames = opt2bSet("-frames", NFILE, fnm);
if (bCalcN)
{
fprintf(stderr, "Will calculate number of different contacts\n");
}
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, FALSE);
fprintf(stderr, "Select group for analysis\n");
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
natoms = isize;
snew(useatoms.atom, natoms);
snew(useatoms.atomname, natoms);
useatoms.nres = 0;
snew(useatoms.resinfo, natoms);
prevres = top.atoms.atom[index[0]].resind;
newres = 0;
for (i = 0; (i < isize); i++)
{
int ii = index[i];
useatoms.atomname[i] = top.atoms.atomname[ii];
if (top.atoms.atom[ii].resind != prevres)
{
prevres = top.atoms.atom[ii].resind;
newres++;
useatoms.resinfo[i] = top.atoms.resinfo[prevres];
if (debug)
{
fprintf(debug, "New residue: atom %5s %5s %6d, index entry %5d, newres %5d\n",
*(top.atoms.resinfo[top.atoms.atom[ii].resind].name),
*(top.atoms.atomname[ii]),
ii, i, newres);
}
}
useatoms.atom[i].resind = newres;
}
useatoms.nres = newres+1;
useatoms.nr = isize;
rndx = res_ndx(&(useatoms));
natm = res_natm(&(useatoms));
nres = useatoms.nres;
fprintf(stderr, "There are %d residues with %d atoms\n", nres, natoms);
snew(resnr, nres);
snew(mdmat, nres);
snew(nmat, nres);
snew(totnmat, nres);
snew(mean_n, nres);
snew(tot_n, nres);
for (i = 0; (i < nres); i++)
{
snew(mdmat[i], nres);
snew(nmat[i], natoms);
snew(totnmat[i], natoms);
resnr[i] = i+1;
}
snew(totmdmat, nres);
for (i = 0; (i < nres); i++)
{
snew(totmdmat[i], nres);
}
trxnat = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
nframes = 0;
rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
gpbc = gmx_rmpbc_init(&top.idef, ePBC, trxnat, box);
if (bFrames)
{
out = opt2FILE("-frames", NFILE, fnm, "w");
}
do
{
gmx_rmpbc(gpbc, trxnat, box, x);
nframes++;
calc_mat(nres, natoms, rndx, x, index, truncate, mdmat, nmat, ePBC, box);
for (i = 0; (i < nres); i++)
{
for (j = 0; (j < natoms); j++)
{
if (nmat[i][j])
{
totnmat[i][j]++;
}
}
}
for (i = 0; (i < nres); i++)
{
for (j = 0; (j < nres); j++)
{
totmdmat[i][j] += mdmat[i][j];
}
}
if (bFrames)
{
sprintf(label, "t=%.0f ps", t);
write_xpm(out, 0, label, "Distance (nm)", "Residue Index", "Residue Index",
nres, nres, resnr, resnr, mdmat, 0, truncate, rlo, rhi, &nlevels);
}
}
while (read_next_x(oenv, status, &t, trxnat, x, box));
fprintf(stderr, "\n");
close_trj(status);
gmx_rmpbc_done(gpbc);
if (bFrames)
{
ffclose(out);
}
fprintf(stderr, "Processed %d frames\n", nframes);
for (i = 0; (i < nres); i++)
{
for (j = 0; (j < nres); j++)
{
totmdmat[i][j] /= nframes;
}
}
write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0, "Mean smallest distance",
"Distance (nm)", "Residue Index", "Residue Index",
nres, nres, resnr, resnr, totmdmat, 0, truncate, rlo, rhi, &nlevels);
if (bCalcN)
{
tot_nmat(nres, natoms, nframes, totnmat, tot_n, mean_n);
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Increase in number of contacts", "Residue", "Ratio", oenv);
fprintf(fp, "@ legend on\n");
fprintf(fp, "@ legend box on\n");
fprintf(fp, "@ legend loctype view\n");
fprintf(fp, "@ legend 0.75, 0.8\n");
fprintf(fp, "@ legend string 0 \"Total/mean\"\n");
fprintf(fp, "@ legend string 1 \"Total\"\n");
fprintf(fp, "@ legend string 2 \"Mean\"\n");
fprintf(fp, "@ legend string 3 \"# atoms\"\n");
fprintf(fp, "@ legend string 4 \"Mean/# atoms\"\n");
fprintf(fp, "#%3s %8s %3s %8s %3s %8s\n",
"res", "ratio", "tot", "mean", "natm", "mean/atm");
for (i = 0; (i < nres); i++)
{
if (mean_n[i] == 0)
{
ratio = 1;
}
else
{
ratio = tot_n[i]/mean_n[i];
}
fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n",
i+1, ratio, tot_n[i], mean_n[i], natm[i], mean_n[i]/natm[i]);
}
ffclose(fp);
}
thanx(stderr);
return 0;
}
int main (int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_protonate[tt] reads (a) conformation(s) and adds all missing",
"hydrogens as defined in [TT]gmx2.ff/aminoacids.hdb[tt]. If only [TT]-s[tt] is",
"specified, this conformation will be protonated, if also [TT]-f[tt]",
"is specified, the conformation(s) will be read from this file, ",
"which can be either a single conformation or a trajectory.",
"[PAR]",
"If a [TT].pdb[tt] file is supplied, residue names might not correspond to",
"to the GROMACS naming conventions, in which case these residues will",
"probably not be properly protonated.",
"[PAR]",
"If an index file is specified, please note that the atom numbers",
"should correspond to the [BB]protonated[bb] state."
};
char title[STRLEN+1];
const char *infile;
char *grpnm;
t_topology top;
int ePBC;
t_atoms *atoms,*iatoms;
t_protonate protdata;
atom_id *index;
t_trxstatus *status;
t_trxstatus *out;
t_trxframe fr,frout;
rvec *x,*ix;
int nidx,natoms,natoms_out;
matrix box;
int i,frame,resind;
gmx_bool bReadMultiple;
output_env_t oenv;
const char *bugs[] = {
"For the moment, only .pdb files are accepted to the -s flag"
};
t_filenm fnm[] = {
{ efTPS, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efTRO, "-o", "protonated", ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME,
NFILE,fnm,0,NULL,asize(desc),desc,asize(bugs),bugs,&oenv);
infile=opt2fn("-s",NFILE,fnm);
read_tps_conf(infile,title,&top,&ePBC,&x,NULL,box,FALSE);
atoms=&(top.atoms);
printf("Select group to process:\n");
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
bReadMultiple = opt2bSet("-f",NFILE,fnm);
if (bReadMultiple) {
infile = opt2fn("-f",NFILE,fnm);
if ( !read_first_frame(oenv,&status, infile, &fr, TRX_NEED_X ) ) {
gmx_fatal(FARGS,"cannot read coordinate file %s",infile);
}
natoms = fr.natoms;
} else {
clear_trxframe(&fr,TRUE);
fr.natoms = atoms->nr;
fr.bTitle = TRUE;
fr.title = title;
fr.bX = TRUE;
fr.x = x;
fr.bBox = TRUE;
copy_mat(box, fr.box);
natoms = fr.natoms;
}
/* check input */
if ( natoms == 0 ) {
gmx_fatal(FARGS,"no atoms in coordinate file %s",infile);
}
if ( natoms > atoms->nr ) {
gmx_fatal(FARGS,"topology with %d atoms does not match "
"coordinates with %d atoms",atoms->nr,natoms);
}
for(i=0; i<nidx; i++) {
if (index[i] > natoms) {
gmx_fatal(FARGS,"An atom number in group %s is larger than the number of "
"atoms (%d) in the coordinate file %s",grpnm,natoms,infile);
}
}
/* get indexed copy of atoms */
snew(iatoms,1);
init_t_atoms(iatoms,nidx,FALSE);
snew(iatoms->atom, iatoms->nr);
resind = 0;
for(i=0; i<nidx; i++) {
iatoms->atom[i] = atoms->atom[index[i]];
iatoms->atomname[i] = atoms->atomname[index[i]];
if ( i>0 && (atoms->atom[index[i]].resind!=atoms->atom[index[i-1]].resind) ) {
resind++;
}
iatoms->atom[i].resind = resind;
iatoms->resinfo[resind] = atoms->resinfo[atoms->atom[index[i]].resind];
/* allocate some space for the rtp name and copy from name */
snew(iatoms->resinfo[resind].rtp,1);
*iatoms->resinfo[resind].rtp = gmx_strdup(*atoms->resinfo[resind].name);
iatoms->nres = max(iatoms->nres, iatoms->atom[i].resind+1);
}
init_t_protonate(&protdata);
out = open_trx(opt2fn("-o",NFILE,fnm),"w");
snew(ix, nidx);
frame=0;
do {
if (debug) {
fprintf(debug,"FRAME %d (%d %g)\n",frame,fr.step,fr.time);
}
/* get indexed copy of x */
for(i=0; i<nidx; i++) {
copy_rvec(fr.x[index[i]], ix[i]);
}
/* protonate */
natoms_out = protonate(&iatoms, &ix, &protdata);
/* setup output frame */
frout = fr;
frout.natoms = natoms_out;
frout.bAtoms = TRUE;
frout.atoms = iatoms;
frout.bV = FALSE;
frout.bF = FALSE;
frout.x = ix;
/* write output */
write_trxframe(out,&frout,NULL);
frame++;
} while ( bReadMultiple && read_next_frame(oenv,status, &fr) );
sfree(ix);
sfree(iatoms);
thanx(stderr);
return 0;
}
int gmx_trjorder(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] orders molecules according to the smallest distance",
"to atoms in a reference group",
"or on z-coordinate (with option [TT]-z[tt]).",
"With distance ordering, it will ask for a group of reference",
"atoms and a group of molecules. For each frame of the trajectory",
"the selected molecules will be reordered according to the shortest",
"distance between atom number [TT]-da[tt] in the molecule and all the",
"atoms in the reference group. The center of mass of the molecules can",
"be used instead of a reference atom by setting [TT]-da[tt] to 0.",
"All atoms in the trajectory are written",
"to the output trajectory.[PAR]",
"[THISMODULE] can be useful for e.g. analyzing the n waters closest to a",
"protein.",
"In that case the reference group would be the protein and the group",
"of molecules would consist of all the water atoms. When an index group",
"of the first n waters is made, the ordered trajectory can be used",
"with any GROMACS program to analyze the n closest waters.",
"[PAR]",
"If the output file is a [REF].pdb[ref] file, the distance to the reference target",
"will be stored in the B-factor field in order to color with e.g. Rasmol.",
"[PAR]",
"With option [TT]-nshell[tt] the number of molecules within a shell",
"of radius [TT]-r[tt] around the reference group are printed."
};
static int na = 3, ref_a = 1;
static real rcut = 0;
static gmx_bool bCOM = FALSE, bZ = FALSE;
t_pargs pa[] = {
{ "-na", FALSE, etINT, {&na},
"Number of atoms in a molecule" },
{ "-da", FALSE, etINT, {&ref_a},
"Atom used for the distance calculation, 0 is COM" },
{ "-com", FALSE, etBOOL, {&bCOM},
"Use the distance to the center of mass of the reference group" },
{ "-r", FALSE, etREAL, {&rcut},
"Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein" },
{ "-z", FALSE, etBOOL, {&bZ},
"Order molecules on z-coordinate" }
};
FILE *fp;
t_trxstatus *out;
t_trxstatus *status;
gmx_bool bNShell, bPDBout;
t_topology top;
int ePBC;
rvec *x, *xsol, xcom, dx;
matrix box;
t_pbc pbc;
gmx_rmpbc_t gpbc;
real t, totmass, mass, rcut2 = 0, n2;
int natoms, nwat, ncut;
char **grpname;
int i, j, d, *isize, isize_ref = 0, isize_sol;
atom_id sa, sr, *swi, **index, *ind_ref = NULL, *ind_sol;
output_env_t oenv;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efTRO, "-o", "ordered", ffOPTWR },
{ efXVG, "-nshell", "nshell", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, TRUE);
sfree(x);
/* get index groups */
printf("Select %sa group of molecules to be ordered:\n",
bZ ? "" : "a group of reference atoms and ");
snew(grpname, 2);
snew(index, 2);
snew(isize, 2);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bZ ? 1 : 2,
isize, index, grpname);
if (!bZ)
{
isize_ref = isize[0];
isize_sol = isize[1];
ind_ref = index[0];
ind_sol = index[1];
}
else
{
isize_sol = isize[0];
ind_sol = index[0];
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
if (natoms > top.atoms.nr)
{
gmx_fatal(FARGS, "Number of atoms in the run input file is larger than in the trjactory");
}
for (i = 0; (i < 2); i++)
{
for (j = 0; (j < isize[i]); j++)
{
if (index[i][j] > natoms)
{
gmx_fatal(FARGS, "An atom number in group %s is larger than the number of atoms in the trajectory");
}
}
}
if ((isize_sol % na) != 0)
{
gmx_fatal(FARGS, "Number of atoms in the molecule group (%d) is not a multiple of na (%d)",
isize[1], na);
}
nwat = isize_sol/na;
if (ref_a > na)
{
gmx_fatal(FARGS, "The reference atom can not be larger than the number of atoms in a molecule");
}
ref_a--;
snew(xsol, nwat);
snew(order, nwat);
snew(swi, natoms);
for (i = 0; (i < natoms); i++)
{
swi[i] = i;
}
out = NULL;
fp = NULL;
bNShell = ((opt2bSet("-nshell", NFILE, fnm)) ||
(opt2parg_bSet("-r", asize(pa), pa)));
bPDBout = FALSE;
if (bNShell)
{
rcut2 = rcut*rcut;
fp = xvgropen(opt2fn("-nshell", NFILE, fnm), "Number of molecules",
"Time (ps)", "N", oenv);
printf("Will compute the number of molecules within a radius of %g\n",
rcut);
}
if (!bNShell || opt2bSet("-o", NFILE, fnm))
{
bPDBout = (fn2ftp(opt2fn("-o", NFILE, fnm)) == efPDB);
if (bPDBout && !top.atoms.pdbinfo)
{
fprintf(stderr, "Creating pdbfino records\n");
snew(top.atoms.pdbinfo, top.atoms.nr);
}
out = open_trx(opt2fn("-o", NFILE, fnm), "w");
}
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
do
{
gmx_rmpbc(gpbc, natoms, box, x);
set_pbc(&pbc, ePBC, box);
if (ref_a == -1)
{
/* Calculate the COM of all solvent molecules */
for (i = 0; i < nwat; i++)
{
totmass = 0;
clear_rvec(xsol[i]);
for (j = 0; j < na; j++)
{
sa = ind_sol[i*na+j];
mass = top.atoms.atom[sa].m;
totmass += mass;
for (d = 0; d < DIM; d++)
{
xsol[i][d] += mass*x[sa][d];
}
}
svmul(1.0/totmass, xsol[i], xsol[i]);
}
}
else
{
/* Copy the reference atom of all solvent molecules */
for (i = 0; i < nwat; i++)
{
copy_rvec(x[ind_sol[i*na+ref_a]], xsol[i]);
}
}
if (bZ)
{
for (i = 0; (i < nwat); i++)
{
sa = ind_sol[na*i];
order[i].i = sa;
order[i].d2 = xsol[i][ZZ];
}
}
else if (bCOM)
{
totmass = 0;
clear_rvec(xcom);
for (i = 0; i < isize_ref; i++)
{
mass = top.atoms.atom[ind_ref[i]].m;
totmass += mass;
for (j = 0; j < DIM; j++)
{
xcom[j] += mass*x[ind_ref[i]][j];
}
}
svmul(1/totmass, xcom, xcom);
for (i = 0; (i < nwat); i++)
{
sa = ind_sol[na*i];
pbc_dx(&pbc, xcom, xsol[i], dx);
order[i].i = sa;
order[i].d2 = norm2(dx);
}
}
else
{
/* Set distance to first atom */
for (i = 0; (i < nwat); i++)
{
sa = ind_sol[na*i];
pbc_dx(&pbc, x[ind_ref[0]], xsol[i], dx);
order[i].i = sa;
order[i].d2 = norm2(dx);
}
for (j = 1; (j < isize_ref); j++)
{
sr = ind_ref[j];
for (i = 0; (i < nwat); i++)
{
pbc_dx(&pbc, x[sr], xsol[i], dx);
n2 = norm2(dx);
if (n2 < order[i].d2)
{
order[i].d2 = n2;
}
}
}
}
if (bNShell)
{
ncut = 0;
for (i = 0; (i < nwat); i++)
{
if (order[i].d2 <= rcut2)
{
ncut++;
}
}
fprintf(fp, "%10.3f %8d\n", t, ncut);
}
if (out)
{
qsort(order, nwat, sizeof(*order), ocomp);
for (i = 0; (i < nwat); i++)
{
for (j = 0; (j < na); j++)
{
swi[ind_sol[na*i]+j] = order[i].i+j;
}
}
/* Store the distance as the B-factor */
if (bPDBout)
{
for (i = 0; (i < nwat); i++)
{
for (j = 0; (j < na); j++)
{
top.atoms.pdbinfo[order[i].i+j].bfac = std::sqrt(order[i].d2);
}
}
}
write_trx(out, natoms, swi, &top.atoms, 0, t, box, x, NULL, NULL);
}
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
if (out)
{
close_trx(out);
}
if (fp)
{
xvgrclose(fp);
}
gmx_rmpbc_done(gpbc);
return 0;
}
int gmx_nmeig(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_nmeig[tt] calculates the eigenvectors/values of a (Hessian) matrix,",
"which can be calculated with [TT]mdrun[tt].",
"The eigenvectors are written to a trajectory file ([TT]-v[tt]).",
"The structure is written first with t=0. The eigenvectors",
"are written as frames with the eigenvector number as timestamp.",
"The eigenvectors can be analyzed with [TT]g_anaeig[tt].",
"An ensemble of structures can be generated from the eigenvectors with",
"[TT]g_nmens[tt]. When mass weighting is used, the generated eigenvectors",
"will be scaled back to plain Cartesian coordinates before generating the",
"output. In this case, they will no longer be exactly orthogonal in the",
"standard Cartesian norm, but in the mass-weighted norm they would be.[PAR]",
"This program can be optionally used to compute quantum corrections to heat capacity",
"and enthalpy by providing an extra file argument [TT]-qcorr[tt]. See the GROMACS",
"manual, Chapter 1, for details. The result includes subtracting a harmonic",
"degree of freedom at the given temperature.",
"The total correction is printed on the terminal screen.",
"The recommended way of getting the corrections out is:[PAR]",
"[TT]g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr][tt][PAR]",
"The [TT]-constr[tt] option should be used when bond constraints were used during the",
"simulation [BB]for all the covalent bonds[bb]. If this is not the case, ",
"you need to analyze the [TT]quant_corr.xvg[tt] file yourself.[PAR]",
"To make things more flexible, the program can also take virtual sites into account",
"when computing quantum corrections. When selecting [TT]-constr[tt] and",
"[TT]-qc[tt], the [TT]-begin[tt] and [TT]-end[tt] options will be set automatically as well.",
"Again, if you think you know it better, please check the [TT]eigenfreq.xvg[tt]",
"output."
};
static gmx_bool bM = TRUE, bCons = FALSE;
static int begin = 1, end = 50, maxspec = 4000;
static real T = 298.15, width = 1;
t_pargs pa[] =
{
{ "-m", FALSE, etBOOL, {&bM},
"Divide elements of Hessian by product of sqrt(mass) of involved "
"atoms prior to diagonalization. This should be used for 'Normal Modes' "
"analysis" },
{ "-first", FALSE, etINT, {&begin},
"First eigenvector to write away" },
{ "-last", FALSE, etINT, {&end},
"Last eigenvector to write away" },
{ "-maxspec", FALSE, etINT, {&maxspec},
"Highest frequency (1/cm) to consider in the spectrum" },
{ "-T", FALSE, etREAL, {&T},
"Temperature for computing quantum heat capacity and enthalpy when using normal mode calculations to correct classical simulations" },
{ "-constr", FALSE, etBOOL, {&bCons},
"If constraints were used in the simulation but not in the normal mode analysis (this is the recommended way of doing it) you will need to set this for computing the quantum corrections." },
{ "-width", FALSE, etREAL, {&width},
"Width (sigma) of the gaussian peaks (1/cm) when generating a spectrum" }
};
FILE *out, *qc, *spec;
int status, trjout;
t_topology top;
gmx_mtop_t mtop;
int ePBC;
rvec *top_x;
matrix box;
real *eigenvalues;
real *eigenvectors;
real rdum, mass_fac, qcvtot, qutot, qcv, qu;
int natoms, ndim, nrow, ncol, count, nharm, nvsite;
char *grpname;
int i, j, k, l, d, gnx;
gmx_bool bSuck;
atom_id *index;
t_tpxheader tpx;
int version, generation;
real value, omega, nu;
real factor_gmx_to_omega2;
real factor_omega_to_wavenumber;
real *spectrum = NULL;
real wfac;
output_env_t oenv;
const char *qcleg[] = {
"Heat Capacity cV (J/mol K)",
"Enthalpy H (kJ/mol)"
};
real * full_hessian = NULL;
gmx_sparsematrix_t * sparse_hessian = NULL;
t_filenm fnm[] = {
{ efMTX, "-f", "hessian", ffREAD },
{ efTPX, NULL, NULL, ffREAD },
{ efXVG, "-of", "eigenfreq", ffWRITE },
{ efXVG, "-ol", "eigenval", ffWRITE },
{ efXVG, "-os", "spectrum", ffOPTWR },
{ efXVG, "-qc", "quant_corr", ffOPTWR },
{ efTRN, "-v", "eigenvec", ffWRITE }
};
#define NFILE asize(fnm)
parse_common_args(&argc, argv, PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
/* Read tpr file for volume and number of harmonic terms */
read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &tpx, TRUE, &version, &generation);
snew(top_x, tpx.natoms);
read_tpx(ftp2fn(efTPX, NFILE, fnm), NULL, box, &natoms,
top_x, NULL, NULL, &mtop);
if (bCons)
{
nharm = get_nharm(&mtop, &nvsite);
}
else
{
nharm = 0;
nvsite = 0;
}
top = gmx_mtop_t_to_t_topology(&mtop);
bM = TRUE;
ndim = DIM*natoms;
if (opt2bSet("-qc", NFILE, fnm))
{
begin = 7+DIM*nvsite;
end = DIM*natoms;
}
if (begin < 1)
{
begin = 1;
}
if (end > ndim)
{
end = ndim;
}
printf("Using begin = %d and end = %d\n", begin, end);
/*open Hessian matrix */
gmx_mtxio_read(ftp2fn(efMTX, NFILE, fnm), &nrow, &ncol, &full_hessian, &sparse_hessian);
/* Memory for eigenvalues and eigenvectors (begin..end) */
snew(eigenvalues, nrow);
snew(eigenvectors, nrow*(end-begin+1));
/* If the Hessian is in sparse format we can calculate max (ndim-1) eigenvectors,
* and they must start at the first one. If this is not valid we convert to full matrix
* storage, but warn the user that we might run out of memory...
*/
if ((sparse_hessian != NULL) && (begin != 1 || end == ndim))
{
if (begin != 1)
{
fprintf(stderr, "Cannot use sparse Hessian with first eigenvector != 1.\n");
}
else if (end == ndim)
{
fprintf(stderr, "Cannot use sparse Hessian to calculate all eigenvectors.\n");
}
fprintf(stderr, "Will try to allocate memory and convert to full matrix representation...\n");
snew(full_hessian, nrow*ncol);
for (i = 0; i < nrow*ncol; i++)
{
full_hessian[i] = 0;
}
for (i = 0; i < sparse_hessian->nrow; i++)
{
for (j = 0; j < sparse_hessian->ndata[i]; j++)
{
k = sparse_hessian->data[i][j].col;
value = sparse_hessian->data[i][j].value;
full_hessian[i*ndim+k] = value;
full_hessian[k*ndim+i] = value;
}
}
gmx_sparsematrix_destroy(sparse_hessian);
sparse_hessian = NULL;
fprintf(stderr, "Converted sparse to full matrix storage.\n");
}
if (full_hessian != NULL)
{
/* Using full matrix storage */
nma_full_hessian(full_hessian, nrow, bM, &top, begin, end,
eigenvalues, eigenvectors);
}
else
{
/* Sparse memory storage, allocate memory for eigenvectors */
snew(eigenvectors, ncol*end);
nma_sparse_hessian(sparse_hessian, bM, &top, end, eigenvalues, eigenvectors);
}
/* check the output, first 6 eigenvalues should be reasonably small */
bSuck = FALSE;
for (i = begin-1; (i < 6); i++)
{
if (fabs(eigenvalues[i]) > 1.0e-3)
{
bSuck = TRUE;
}
}
if (bSuck)
{
fprintf(stderr, "\nOne of the lowest 6 eigenvalues has a non-zero value.\n");
fprintf(stderr, "This could mean that the reference structure was not\n");
fprintf(stderr, "properly energy minimized.\n");
}
/* now write the output */
fprintf (stderr, "Writing eigenvalues...\n");
out = xvgropen(opt2fn("-ol", NFILE, fnm),
"Eigenvalues", "Eigenvalue index", "Eigenvalue [Gromacs units]",
oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
if (bM)
{
fprintf(out, "@ subtitle \"mass weighted\"\n");
}
else
{
fprintf(out, "@ subtitle \"not mass weighted\"\n");
}
}
for (i = 0; i <= (end-begin); i++)
{
fprintf (out, "%6d %15g\n", begin+i, eigenvalues[i]);
}
ffclose(out);
if (opt2bSet("-qc", NFILE, fnm))
{
qc = xvgropen(opt2fn("-qc", NFILE, fnm), "Quantum Corrections", "Eigenvector index", "", oenv);
xvgr_legend(qc, asize(qcleg), qcleg, oenv);
qcvtot = qutot = 0;
}
else
{
qc = NULL;
}
printf("Writing eigenfrequencies - negative eigenvalues will be set to zero.\n");
out = xvgropen(opt2fn("-of", NFILE, fnm),
"Eigenfrequencies", "Eigenvector index", "Wavenumber [cm\\S-1\\N]",
oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
if (bM)
{
fprintf(out, "@ subtitle \"mass weighted\"\n");
}
else
{
fprintf(out, "@ subtitle \"not mass weighted\"\n");
}
}
/* Spectrum ? */
spec = NULL;
if (opt2bSet("-os", NFILE, fnm) && (maxspec > 0))
{
snew(spectrum, maxspec);
spec = xvgropen(opt2fn("-os", NFILE, fnm),
"Vibrational spectrum based on harmonic approximation",
"\\f{12}w\\f{4} (cm\\S-1\\N)",
"Intensity [Gromacs units]",
oenv);
for (i = 0; (i < maxspec); i++)
{
spectrum[i] = 0;
}
}
/* Gromacs units are kJ/(mol*nm*nm*amu),
* where amu is the atomic mass unit.
*
* For the eigenfrequencies we want to convert this to spectroscopic absorption
* wavenumbers given in cm^(-1), which is the frequency divided by the speed of
* light. Do this by first converting to omega^2 (units 1/s), take the square
* root, and finally divide by the speed of light (nm/ps in gromacs).
*/
factor_gmx_to_omega2 = 1.0E21/(AVOGADRO*AMU);
factor_omega_to_wavenumber = 1.0E-5/(2.0*M_PI*SPEED_OF_LIGHT);
for (i = begin; (i <= end); i++)
{
value = eigenvalues[i-begin];
if (value < 0)
{
value = 0;
}
omega = sqrt(value*factor_gmx_to_omega2);
nu = 1e-12*omega/(2*M_PI);
value = omega*factor_omega_to_wavenumber;
fprintf (out, "%6d %15g\n", i, value);
if (NULL != spec)
{
wfac = eigenvalues[i-begin]/(width*sqrt(2*M_PI));
for (j = 0; (j < maxspec); j++)
{
spectrum[j] += wfac*exp(-sqr(j-value)/(2*sqr(width)));
}
}
if (NULL != qc)
{
qcv = cv_corr(nu, T);
qu = u_corr(nu, T);
if (i > end-nharm)
{
qcv += BOLTZ*KILO;
qu += BOLTZ*T;
}
fprintf (qc, "%6d %15g %15g\n", i, qcv, qu);
qcvtot += qcv;
qutot += qu;
}
}
ffclose(out);
if (NULL != spec)
{
for (j = 0; (j < maxspec); j++)
{
fprintf(spec, "%10g %10g\n", 1.0*j, spectrum[j]);
}
ffclose(spec);
}
if (NULL != qc)
{
printf("Quantum corrections for harmonic degrees of freedom\n");
printf("Use appropriate -first and -last options to get reliable results.\n");
printf("There were %d constraints and %d vsites in the simulation\n",
nharm, nvsite);
printf("Total correction to cV = %g J/mol K\n", qcvtot);
printf("Total correction to H = %g kJ/mol\n", qutot);
ffclose(qc);
please_cite(stdout, "Caleman2011b");
}
/* Writing eigenvectors. Note that if mass scaling was used, the eigenvectors
* were scaled back from mass weighted cartesian to plain cartesian in the
* nma_full_hessian() or nma_sparse_hessian() routines. Mass scaled vectors
* will not be strictly orthogonal in plain cartesian scalar products.
*/
write_eigenvectors(opt2fn("-v", NFILE, fnm), natoms, eigenvectors, FALSE, begin, end,
eWXR_NO, NULL, FALSE, top_x, bM, eigenvalues);
thanx(stderr);
return 0;
}
int gmx_gyrate(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the radius of gyration of a molecule",
"and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
"as a function of time. The atoms are explicitly mass weighted.[PAR]",
"The axis components corresponds to the mass-weighted root-mean-square",
"of the radii components orthogonal to each axis, for example:[PAR]",
"Rg(x) = sqrt((sum_i m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).[PAR]",
"With the [TT]-nmol[tt] option the radius of gyration will be calculated",
"for multiple molecules by splitting the analysis group in equally",
"sized parts.[PAR]",
"With the option [TT]-nz[tt] 2D radii of gyration in the [IT]x-y[it] plane",
"of slices along the [IT]z[it]-axis are calculated."
};
static int nmol = 1, nz = 0;
static gmx_bool bQ = FALSE, bRot = FALSE, bMOI = FALSE;
t_pargs pa[] = {
{ "-nmol", FALSE, etINT, {&nmol},
"The number of molecules to analyze" },
{ "-q", FALSE, etBOOL, {&bQ},
"Use absolute value of the charge of an atom as weighting factor instead of mass" },
{ "-p", FALSE, etBOOL, {&bRot},
"Calculate the radii of gyration about the principal axes." },
{ "-moi", FALSE, etBOOL, {&bMOI},
"Calculate the moments of inertia (defined by the principal axes)." },
{ "-nz", FALSE, etINT, {&nz},
"Calculate the 2D radii of gyration of this number of slices along the z-axis" },
};
FILE *out;
t_trxstatus *status;
t_topology top;
int ePBC;
rvec *x, *x_s;
rvec xcm, gvec, gvec1;
matrix box, trans;
gmx_bool bACF;
real **moi_trans = NULL;
int max_moi = 0, delta_moi = 100;
rvec d, d1; /* eigenvalues of inertia tensor */
real t, t0, tm, gyro;
int natoms;
char *grpname;
int j, m, gnx, nam, mol;
atom_id *index;
gmx_output_env_t *oenv;
gmx_rmpbc_t gpbc = NULL;
const char *leg[] = { "Rg", "Rg\\sX\\N", "Rg\\sY\\N", "Rg\\sZ\\N" };
const char *legI[] = { "Itot", "I1", "I2", "I3" };
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "gyrate", ffWRITE },
{ efXVG, "-acf", "moi-acf", ffOPTWR },
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bACF = opt2bSet("-acf", NFILE, fnm);
if (bACF && nmol != 1)
{
gmx_fatal(FARGS, "Can only do acf with nmol=1");
}
bRot = bRot || bMOI || bACF;
/*
if (nz > 0)
bMOI = TRUE;
*/
if (bRot)
{
printf("Will rotate system along principal axes\n");
snew(moi_trans, DIM);
}
if (bMOI)
{
printf("Will print moments of inertia\n");
bQ = FALSE;
}
if (bQ)
{
printf("Will print radius normalised by charge\n");
}
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, TRUE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
if (nmol > gnx || gnx % nmol != 0)
{
gmx_fatal(FARGS, "The number of atoms in the group (%d) is not a multiple of nmol (%d)", gnx, nmol);
}
nam = gnx/nmol;
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(x_s, natoms);
j = 0;
t0 = t;
if (bQ)
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Radius of Charge (total and around axes)", "Time (ps)", "Rg (nm)", oenv);
}
else if (bMOI)
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Moments of inertia (total and around axes)", "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
}
else
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Radius of gyration (total and around axes)", "Time (ps)", "Rg (nm)", oenv);
}
if (bMOI)
{
xvgr_legend(out, NLEG, legI, oenv);
}
else
{
if (bRot)
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "@ subtitle \"Axes are principal component axes\"\n");
}
}
xvgr_legend(out, NLEG, leg, oenv);
}
if (nz == 0)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
}
do
{
if (nz == 0)
{
gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
}
gyro = 0;
clear_rvec(gvec);
clear_rvec(gvec1);
clear_rvec(d);
clear_rvec(d1);
for (mol = 0; mol < nmol; mol++)
{
tm = sub_xcm(nz == 0 ? x_s : x, nam, index+mol*nam, top.atoms.atom, xcm, bQ);
if (nz == 0)
{
gyro += calc_gyro(x_s, nam, index+mol*nam, top.atoms.atom,
tm, gvec1, d1, bQ, bRot, bMOI, trans);
}
else
{
calc_gyro_z(x, box, nam, index+mol*nam, top.atoms.atom, nz, t, out);
}
rvec_inc(gvec, gvec1);
rvec_inc(d, d1);
}
if (nmol > 0)
{
gyro /= nmol;
svmul(1.0/nmol, gvec, gvec);
svmul(1.0/nmol, d, d);
}
if (nz == 0)
{
if (bRot)
{
if (j >= max_moi)
{
max_moi += delta_moi;
for (m = 0; (m < DIM); m++)
{
srenew(moi_trans[m], max_moi*DIM);
}
}
for (m = 0; (m < DIM); m++)
{
copy_rvec(trans[m], moi_trans[m]+DIM*j);
}
fprintf(out, "%10g %10g %10g %10g %10g\n",
t, gyro, d[XX], d[YY], d[ZZ]);
}
else
{
fprintf(out, "%10g %10g %10g %10g %10g\n",
t, gyro, gvec[XX], gvec[YY], gvec[ZZ]);
}
}
j++;
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
if (nz == 0)
{
gmx_rmpbc_done(gpbc);
}
xvgrclose(out);
if (bACF)
{
int mode = eacVector;
do_autocorr(opt2fn("-acf", NFILE, fnm), oenv,
"Moment of inertia vector ACF",
j, 3, moi_trans, (t-t0)/j, mode, FALSE);
do_view(oenv, opt2fn("-acf", NFILE, fnm), "-nxy");
}
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
return 0;
}
int gmx_disre(int argc,char *argv[])
{
const char *desc[] = {
"g_disre computes violations of distance restraints.",
"If necessary all protons can be added to a protein molecule ",
"using the protonate program.[PAR]",
"The program always",
"computes the instantaneous violations rather than time-averaged,",
"because this analysis is done from a trajectory file afterwards",
"it does not make sense to use time averaging. However,",
"the time averaged values per restraint are given in the log file.[PAR]",
"An index file may be used to select specific restraints for",
"printing.[PAR]",
"When the optional[TT]-q[tt] flag is given a pdb file coloured by the",
"amount of average violations.[PAR]",
"When the [TT]-c[tt] option is given, an index file will be read",
"containing the frames in your trajectory corresponding to the clusters",
"(defined in another manner) that you want to analyze. For these clusters",
"the program will compute average violations using the third power",
"averaging algorithm and print them in the log file."
};
static int ntop = 0;
static int nlevels = 20;
static real max_dr = 0;
static gmx_bool bThird = TRUE;
t_pargs pa[] = {
{ "-ntop", FALSE, etINT, {&ntop},
"Number of large violations that are stored in the log file every step" },
{ "-maxdr", FALSE, etREAL, {&max_dr},
"Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data." },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of levels in the matrix output" },
{ "-third", FALSE, etBOOL, {&bThird},
"Use inverse third power averaging or linear for matrix output" }
};
FILE *out=NULL,*aver=NULL,*numv=NULL,*maxxv=NULL,*xvg=NULL;
t_tpxheader header;
t_inputrec ir;
gmx_mtop_t mtop;
rvec *xtop;
gmx_localtop_t *top;
t_atoms *atoms=NULL;
t_forcerec *fr;
t_fcdata fcd;
t_nrnb nrnb;
t_commrec *cr;
t_graph *g;
int ntopatoms,natoms,i,j,kkk;
t_trxstatus *status;
real t;
rvec *x,*f,*xav=NULL;
matrix box;
gmx_bool bPDB;
int isize;
atom_id *index=NULL,*ind_fit=NULL;
char *grpname;
t_cluster_ndx *clust=NULL;
t_dr_result dr,*dr_clust=NULL;
char **leg;
real *vvindex=NULL,*w_rls=NULL;
t_mdatoms *mdatoms;
t_pbc pbc,*pbc_null;
int my_clust;
FILE *fplog;
output_env_t oenv;
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efXVG, "-ds", "drsum", ffWRITE },
{ efXVG, "-da", "draver", ffWRITE },
{ efXVG, "-dn", "drnum", ffWRITE },
{ efXVG, "-dm", "drmax", ffWRITE },
{ efXVG, "-dr", "restr", ffWRITE },
{ efLOG, "-l", "disres", ffWRITE },
{ efNDX, NULL, "viol", ffOPTRD },
{ efPDB, "-q", "viol", ffOPTWR },
{ efNDX, "-c", "clust", ffOPTRD },
{ efXPM, "-x", "matrix", ffOPTWR }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,FALSE,0,&fplog);
if (ntop)
init5(ntop);
read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&header,FALSE,NULL,NULL);
snew(xtop,header.natoms);
read_tpx(ftp2fn(efTPX,NFILE,fnm),&ir,box,&ntopatoms,xtop,NULL,NULL,&mtop);
bPDB = opt2bSet("-q",NFILE,fnm);
if (bPDB) {
snew(xav,ntopatoms);
snew(ind_fit,ntopatoms);
snew(w_rls,ntopatoms);
for(kkk=0; (kkk<ntopatoms); kkk++) {
w_rls[kkk] = 1;
ind_fit[kkk] = kkk;
}
snew(atoms,1);
*atoms = gmx_mtop_global_atoms(&mtop);
if (atoms->pdbinfo == NULL) {
snew(atoms->pdbinfo,atoms->nr);
}
}
top = gmx_mtop_generate_local_top(&mtop,&ir);
g = NULL;
pbc_null = NULL;
if (ir.ePBC != epbcNONE) {
if (ir.bPeriodicMols)
pbc_null = &pbc;
else
g = mk_graph(fplog,&top->idef,0,mtop.natoms,FALSE,FALSE);
}
if (ftp2bSet(efNDX,NFILE,fnm)) {
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
xvg=xvgropen(opt2fn("-dr",NFILE,fnm),"Inidividual Restraints","Time (ps)",
"nm",oenv);
snew(vvindex,isize);
snew(leg,isize);
for(i=0; (i<isize); i++) {
index[i]++;
snew(leg[i],12);
sprintf(leg[i],"index %d",index[i]);
}
xvgr_legend(xvg,isize,(const char**)leg,oenv);
}
else
isize=0;
ir.dr_tau=0.0;
init_disres(fplog,&mtop,&ir,NULL,FALSE,&fcd,NULL);
natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
snew(f,5*natoms);
init_dr_res(&dr,fcd.disres.nres);
if (opt2bSet("-c",NFILE,fnm)) {
clust = cluster_index(fplog,opt2fn("-c",NFILE,fnm));
snew(dr_clust,clust->clust->nr+1);
for(i=0; (i<=clust->clust->nr); i++)
init_dr_res(&dr_clust[i],fcd.disres.nres);
}
else {
out =xvgropen(opt2fn("-ds",NFILE,fnm),
"Sum of Violations","Time (ps)","nm",oenv);
aver=xvgropen(opt2fn("-da",NFILE,fnm),
"Average Violation","Time (ps)","nm",oenv);
numv=xvgropen(opt2fn("-dn",NFILE,fnm),
"# Violations","Time (ps)","#",oenv);
maxxv=xvgropen(opt2fn("-dm",NFILE,fnm),
"Largest Violation","Time (ps)","nm",oenv);
}
mdatoms = init_mdatoms(fplog,&mtop,ir.efep!=efepNO);
atoms2md(&mtop,&ir,0,NULL,0,mtop.natoms,mdatoms);
update_mdatoms(mdatoms,ir.init_lambda);
fr = mk_forcerec();
fprintf(fplog,"Made forcerec\n");
init_forcerec(fplog,oenv,fr,NULL,&ir,&mtop,cr,box,FALSE,NULL,NULL,NULL,
FALSE,-1);
init_nrnb(&nrnb);
if (ir.ePBC != epbcNONE)
gpbc = gmx_rmpbc_init(&top->idef,ir.ePBC,natoms,box);
j=0;
do {
if (ir.ePBC != epbcNONE) {
if (ir.bPeriodicMols)
set_pbc(&pbc,ir.ePBC,box);
else
gmx_rmpbc(gpbc,natoms,box,x);
}
if (clust) {
if (j > clust->maxframe)
gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file. t = %8f\n",t);
my_clust = clust->inv_clust[j];
range_check(my_clust,0,clust->clust->nr);
check_viol(fplog,cr,&(top->idef.il[F_DISRES]),
top->idef.iparams,top->idef.functype,
x,f,fr,pbc_null,g,dr_clust,my_clust,isize,index,vvindex,&fcd);
}
else
check_viol(fplog,cr,&(top->idef.il[F_DISRES]),
top->idef.iparams,top->idef.functype,
x,f,fr,pbc_null,g,&dr,0,isize,index,vvindex,&fcd);
if (bPDB) {
reset_x(atoms->nr,ind_fit,atoms->nr,NULL,x,w_rls);
do_fit(atoms->nr,w_rls,x,x);
if (j == 0) {
/* Store the first frame of the trajectory as 'characteristic'
* for colouring with violations.
*/
for(kkk=0; (kkk<atoms->nr); kkk++)
copy_rvec(x[kkk],xav[kkk]);
}
}
if (!clust) {
if (isize > 0) {
fprintf(xvg,"%10g",t);
for(i=0; (i<isize); i++)
fprintf(xvg," %10g",vvindex[i]);
fprintf(xvg,"\n");
}
fprintf(out, "%10g %10g\n",t,dr.sumv);
fprintf(aver, "%10g %10g\n",t,dr.averv);
fprintf(maxxv,"%10g %10g\n",t,dr.maxv);
fprintf(numv, "%10g %10d\n",t,dr.nv);
}
j++;
} while (read_next_x(oenv,status,&t,natoms,x,box));
close_trj(status);
if (ir.ePBC != epbcNONE)
gmx_rmpbc_done(gpbc);
if (clust) {
dump_clust_stats(fplog,fcd.disres.nres,&(top->idef.il[F_DISRES]),
top->idef.iparams,clust->clust,dr_clust,
clust->grpname,isize,index);
}
else {
dump_stats(fplog,j,fcd.disres.nres,&(top->idef.il[F_DISRES]),
top->idef.iparams,&dr,isize,index,
bPDB ? atoms : NULL);
if (bPDB) {
write_sto_conf(opt2fn("-q",NFILE,fnm),
"Coloured by average violation in Angstrom",
atoms,xav,NULL,ir.ePBC,box);
}
dump_disre_matrix(opt2fn_null("-x",NFILE,fnm),&dr,fcd.disres.nres,
j,&top->idef,&mtop,max_dr,nlevels,bThird);
ffclose(out);
ffclose(aver);
ffclose(numv);
ffclose(maxxv);
if (isize > 0) {
ffclose(xvg);
do_view(oenv,opt2fn("-dr",NFILE,fnm),"-nxy");
}
do_view(oenv,opt2fn("-dn",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-da",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-ds",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-dm",NFILE,fnm),"-nxy");
}
thanx(stderr);
if (gmx_parallel_env_initialized())
gmx_finalize();
gmx_log_close(fplog);
return 0;
}
int gmx_order(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the order parameter per atom for carbon tails. For atom i the",
"vector i-1, i+1 is used together with an axis. ",
"The index file should contain only the groups to be used for calculations,",
"with each group of equivalent carbons along the relevant acyl chain in its own",
"group. There should not be any generic groups (like System, Protein) in the index",
"file to avoid confusing the program (this is not relevant to tetrahedral order",
"parameters however, which only work for water anyway).[PAR]",
"[THISMODULE] can also give all",
"diagonal elements of the order tensor and even calculate the deuterium",
"order parameter Scd (default). If the option [TT]-szonly[tt] is given, only one",
"order tensor component (specified by the [TT]-d[tt] option) is given and the",
"order parameter per slice is calculated as well. If [TT]-szonly[tt] is not",
"selected, all diagonal elements and the deuterium order parameter is",
"given.[PAR]"
"The tetrahedrality order parameters can be determined",
"around an atom. Both angle an distance order parameters are calculated. See",
"P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
"for more details."
};
static int nslices = 1; /* nr of slices defined */
static gmx_bool bSzonly = FALSE; /* True if only Sz is wanted */
static gmx_bool bUnsat = FALSE; /* True if carbons are unsat. */
static const char *normal_axis[] = { NULL, "z", "x", "y", NULL };
static gmx_bool permolecule = FALSE; /*compute on a per-molecule basis */
static gmx_bool radial = FALSE; /*compute a radial membrane normal */
static gmx_bool distcalc = FALSE; /*calculate distance from a reference group */
t_pargs pa[] = {
{ "-d", FALSE, etENUM, {normal_axis},
"Direction of the normal on the membrane" },
{ "-sl", FALSE, etINT, {&nslices},
"Calculate order parameter as function of box length, dividing the box"
" into this number of slices." },
{ "-szonly", FALSE, etBOOL, {&bSzonly},
"Only give Sz element of order tensor. (axis can be specified with [TT]-d[tt])" },
{ "-unsat", FALSE, etBOOL, {&bUnsat},
"Calculate order parameters for unsaturated carbons. Note that this can"
"not be mixed with normal order parameters." },
{ "-permolecule", FALSE, etBOOL, {&permolecule},
"Compute per-molecule Scd order parameters" },
{ "-radial", FALSE, etBOOL, {&radial},
"Compute a radial membrane normal" },
{ "-calcdist", FALSE, etBOOL, {&distcalc},
"Compute distance from a reference" },
};
rvec *order; /* order par. for each atom */
real **slOrder; /* same, per slice */
real slWidth = 0.0; /* width of a slice */
char **grpname; /* groupnames */
int ngrps, /* nr. of groups */
i,
axis = 0; /* normal axis */
t_topology *top; /* topology */
int ePBC;
atom_id *index, /* indices for a */
*a; /* atom numbers in each group */
t_blocka *block; /* data from index file */
t_filenm fnm[] = { /* files for g_order */
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, "-n", NULL, ffREAD }, /* index file */
{ efNDX, "-nr", NULL, ffREAD }, /* index for radial axis calculation */
{ efTPR, NULL, NULL, ffREAD }, /* topology file */
{ efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
{ efXVG, "-od", "deuter", ffWRITE }, /* xvgr output file */
{ efPDB, "-ob", NULL, ffWRITE }, /* write Scd as B factors to PDB if permolecule */
{ efXVG, "-os", "sliced", ffWRITE }, /* xvgr output file */
{ efXVG, "-Sg", "sg-ang", ffOPTWR }, /* xvgr output file */
{ efXVG, "-Sk", "sk-dist", ffOPTWR }, /* xvgr output file */
{ efXVG, "-Sgsl", "sg-ang-slice", ffOPTWR }, /* xvgr output file */
{ efXVG, "-Sksl", "sk-dist-slice", ffOPTWR }, /* xvgr output file */
};
gmx_bool bSliced = FALSE; /* True if box is sliced */
#define NFILE asize(fnm)
real **distvals = NULL;
const char *sgfnm, *skfnm, *ndxfnm, *tpsfnm, *trxfnm;
gmx_output_env_t *oenv;
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
if (nslices < 1)
{
gmx_fatal(FARGS, "Can not have nslices < 1");
}
sgfnm = opt2fn_null("-Sg", NFILE, fnm);
skfnm = opt2fn_null("-Sk", NFILE, fnm);
ndxfnm = opt2fn_null("-n", NFILE, fnm);
tpsfnm = ftp2fn(efTPR, NFILE, fnm);
trxfnm = ftp2fn(efTRX, NFILE, fnm);
/* Calculate axis */
GMX_RELEASE_ASSERT(normal_axis[0] != NULL, "Options inconsistency; normal_axis[0] is NULL");
if (std::strcmp(normal_axis[0], "x") == 0)
{
axis = XX;
}
else if (std::strcmp(normal_axis[0], "y") == 0)
{
axis = YY;
}
else if (std::strcmp(normal_axis[0], "z") == 0)
{
axis = ZZ;
}
else
{
gmx_fatal(FARGS, "Invalid axis, use x, y or z");
}
switch (axis)
{
case 0:
fprintf(stderr, "Taking x axis as normal to the membrane\n");
break;
case 1:
fprintf(stderr, "Taking y axis as normal to the membrane\n");
break;
case 2:
fprintf(stderr, "Taking z axis as normal to the membrane\n");
break;
}
/* tetraheder order parameter */
if (skfnm || sgfnm)
{
/* If either of theoptions is set we compute both */
sgfnm = opt2fn("-Sg", NFILE, fnm);
skfnm = opt2fn("-Sk", NFILE, fnm);
calc_tetra_order_parm(ndxfnm, tpsfnm, trxfnm, sgfnm, skfnm, nslices, axis,
opt2fn("-Sgsl", NFILE, fnm), opt2fn("-Sksl", NFILE, fnm),
oenv);
/* view xvgr files */
do_view(oenv, opt2fn("-Sg", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-Sk", NFILE, fnm), NULL);
if (nslices > 1)
{
do_view(oenv, opt2fn("-Sgsl", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-Sksl", NFILE, fnm), NULL);
}
}
else
{
/* tail order parameter */
if (nslices > 1)
{
bSliced = TRUE;
fprintf(stderr, "Dividing box in %d slices.\n\n", nslices);
}
if (bSzonly)
{
fprintf(stderr, "Only calculating Sz\n");
}
if (bUnsat)
{
fprintf(stderr, "Taking carbons as unsaturated!\n");
}
top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
block = init_index(ftp2fn(efNDX, NFILE, fnm), &grpname);
index = block->index; /* get indices from t_block block */
a = block->a; /* see block.h */
ngrps = block->nr;
if (permolecule)
{
nslices = index[1] - index[0]; /*I think this assumes contiguous lipids in topology*/
fprintf(stderr, "Calculating Scd order parameters for each of %d molecules\n", nslices);
}
if (radial)
{
fprintf(stderr, "Calculating radial distances\n");
if (!permolecule)
{
gmx_fatal(FARGS, "Cannot yet output radial distances without permolecule\n");
}
}
/* show atomtypes, to check if index file is correct */
print_types(index, a, ngrps, grpname, top);
calc_order(ftp2fn(efTRX, NFILE, fnm), index, a, &order,
&slOrder, &slWidth, nslices, bSliced, bUnsat,
top, ePBC, ngrps, axis, permolecule, radial, distcalc, opt2fn_null("-nr", NFILE, fnm), &distvals, oenv);
if (radial)
{
ngrps--; /*don't print the last group--was used for
center-of-mass determination*/
}
order_plot(order, slOrder, opt2fn("-o", NFILE, fnm), opt2fn("-os", NFILE, fnm),
opt2fn("-od", NFILE, fnm), ngrps, nslices, slWidth, bSzonly, permolecule, distvals, oenv);
if (opt2bSet("-ob", NFILE, fnm))
{
if (!permolecule)
{
fprintf(stderr,
"Won't write B-factors with averaged order parameters; use -permolecule\n");
}
else
{
write_bfactors(fnm, NFILE, index, a, nslices, ngrps, slOrder, top, distvals, oenv);
}
}
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL); /* view xvgr file */
do_view(oenv, opt2fn("-os", NFILE, fnm), NULL); /* view xvgr file */
do_view(oenv, opt2fn("-od", NFILE, fnm), NULL); /* view xvgr file */
}
if (distvals != NULL)
{
for (i = 0; i < nslices; ++i)
{
sfree(distvals[i]);
}
sfree(distvals);
}
return 0;
}
//! Implements C-style main function for mdrun
int gmx_mdrun(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"test particle insertion or (re)calculation of energies.",
"Normal mode analysis is another option. In this case [TT]mdrun[tt]",
"builds a Hessian matrix from single conformation.",
"For usual Normal Modes-like calculations, make sure that",
"the structure provided is properly energy-minimized.",
"The generated matrix can be diagonalized by [gmx-nmeig].[PAR]",
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over ranks if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
"Running mdrun efficiently in parallel is a complex topic topic,",
"many aspects of which are covered in the online User Guide. You",
"should look there for practical advice on using many of the options",
"available in mdrun.[PAR]",
"ED (essential dynamics) sampling and/or additional flooding potentials",
"are switched on by using the [TT]-ei[tt] flag followed by an [REF].edi[ref]",
"file. The [REF].edi[ref] file can be produced with the [TT]make_edi[tt] tool",
"or by using options in the essdyn menu of the WHAT IF program.",
"[TT]mdrun[tt] produces a [REF].xvg[ref] output file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"[REF].mdp[ref] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
"When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type used, a table file name must",
"be given. For the topology to work, a file name given here must match a",
"character sequence before the file extension. That sequence is: an underscore,",
"then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals,",
"and finally the matching table number index used in the topology.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [REF].mdp[ref] file.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability.",
"[PAR]",
"The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
"a protein into a membrane. This module requires a number of settings",
"that are provided in a data file that is the argument of this option.",
"For more details in membrane embedding, see the documentation in the",
"user guide. The options [TT]-mn[tt] and [TT]-mp[tt] are used to provide",
"the index and topology files used for the embedding.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
"be printed to stderr. It will also terminate the run when non-finite",
"forces are present.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"unless option [TT]-cpt[tt] is set to -1.",
"The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
"make sure that a recent state of the system is always available,",
"even when the simulation is terminated while writing a checkpoint.",
"With [TT]-cpnum[tt] all checkpoint files are kept and appended",
"with the step number.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, GROMACS just assumes a normal run and",
"starts from the first step of the [REF].tpr[ref] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
"There are three scenarios with [TT]-cpi[tt]:[PAR]",
"[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
"[TT]*[tt] all files are present with names and checksums matching those stored",
"in the checkpoint file: files are appended[PAR]",
"[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
"and will be overwritten, unless its name does not match",
"the [TT]-cpo[tt] option.",
"[PAR]",
"With checkpointing the output is appended to previously written",
"output files, unless [TT]-noappend[tt] is used or none of the previous",
"output files are present (except for the checkpoint file).",
"The integrity of the files to be appended is verified using checksums",
"which are stored in the checkpoint file. This ensures that output can",
"not be mixed up or corrupted due to file appending. When only some",
"of the previous output files are present, a fatal error is generated",
"and no old output files are modified and no new output files are opened.",
"The result with appending will be the same as from a single run.",
"The contents will be binary identical, unless you use a different number",
"of ranks or dynamic load balancing or the FFT library uses optimizations",
"through timing.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
"exceeds [TT]-maxh[tt]\\*0.99 hours. This option is particularly useful in",
"combination with setting [TT]nsteps[tt] to -1 either in the mdp or using the",
"similarly named command line option. This results in an infinite run,",
"terminated only when the time limit set by [TT]-maxh[tt] is reached (if any)"
"or upon receiving a signal."
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will stop as soon as",
"checkpoint file can be written, i.e. after the next global communication step.",
"When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
"pressed), it will stop at the next neighbor search step or at the",
"second global communication step, whichever happens later.",
"In both cases all the usual output will be written to file.",
"When running with MPI, a signal to one of the [TT]mdrun[tt] ranks",
"is sufficient, this signal should not be sent to mpirun or",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"Interactive molecular dynamics (IMD) can be activated by using at least one",
"of the three IMD switches: The [TT]-imdterm[tt] switch allows one to terminate",
"the simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
"[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
"IMD remote can be turned on by [TT]-imdpull[tt].",
"The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
"file pointed to by [TT]-if[tt] contains atom indices and forces if IMD",
"pulling is used."
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
};
t_commrec *cr;
t_filenm fnm[] = {
{ efTPR, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efCOMPRESSED, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD | ffALLOW_MISSING },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRDMULT },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efXVG, "-eo", "edsam", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles", ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque", ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efRND, "-multidir", NULL, ffOPTRDMULT},
{ efDAT, "-membed", "membed", ffOPTRD },
{ efTOP, "-mp", "membed", ffOPTRD },
{ efNDX, "-mn", "membed", ffOPTRD },
{ efXVG, "-if", "imdforces", ffOPTWR },
{ efXVG, "-swap", "swapions", ffOPTWR }
};
const int NFILE = asize(fnm);
/* Command line options ! */
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bTunePME = TRUE;
gmx_bool bVerbose = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
gmx_bool bIMDwait = FALSE;
gmx_bool bIMDterm = FALSE;
gmx_bool bIMDpull = FALSE;
int npme = -1;
int nstlist = 0;
int nmultisim = 0;
int nstglobalcomm = -1;
int repl_ex_nst = 0;
int repl_ex_seed = -1;
int repl_ex_nex = 0;
int nstepout = 100;
int resetstep = -1;
gmx_int64_t nsteps = -2; /* the value -2 means that the mdp option will be used */
int imdport = 8888; /* can be almost anything, 8888 is easy to remember */
rvec realddxyz = {0, 0, 0};
const char *ddrank_opt[ddrankorderNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
const char *thread_aff_opt[threadaffNR+1] =
{ NULL, "auto", "on", "off", NULL };
const char *nbpu_opt[] =
{ NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
real cpt_period = 15.0, max_hours = -1;
gmx_bool bTryToAppendFiles = TRUE;
gmx_bool bKeepAndNumCPT = FALSE;
gmx_bool bResetCountersHalfWay = FALSE;
gmx_output_env_t *oenv = NULL;
/* Non transparent initialization of a complex gmx_hw_opt_t struct.
* But unfortunately we are not allowed to call a function here,
* since declarations follow below.
*/
gmx_hw_opt_t hw_opt = {
0, 0, 0, 0, threadaffSEL, 0, 0,
{ NULL, FALSE, 0, NULL }
};
t_pargs pa[] = {
{ "-dd", FALSE, etRVEC, {&realddxyz},
"Domain decomposition grid, 0 is optimize" },
{ "-ddorder", FALSE, etENUM, {ddrank_opt},
"DD rank order" },
{ "-npme", FALSE, etINT, {&npme},
"Number of separate ranks to be used for PME, -1 is guess" },
{ "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
"Total number of threads to start (0 is guess)" },
{ "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
"Number of thread-MPI threads to start (0 is guess)" },
{ "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
"Number of OpenMP threads per MPI rank to start (0 is guess)" },
{ "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
"Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
{ "-pin", FALSE, etENUM, {thread_aff_opt},
"Whether mdrun should try to set thread affinities" },
{ "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
"The lowest logical core number to which mdrun should pin the first thread" },
{ "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
"Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
{ "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
"List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
"Check for all bonded interactions with DD" },
{ "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
{ "-rdd", FALSE, etREAL, {&rdd},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
{ "-rcon", FALSE, etREAL, {&rconstr},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
{ "-dlb", FALSE, etENUM, {dddlb_opt},
"Dynamic load balancing (with DD)" },
{ "-dds", FALSE, etREAL, {&dlb_scale},
"Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
"provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
{ "-ddcsx", FALSE, etSTR, {&ddcsx},
"HIDDENA string containing a vector of the relative sizes in the x "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-ddcsy", FALSE, etSTR, {&ddcsy},
"HIDDENA string containing a vector of the relative sizes in the y "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-ddcsz", FALSE, etSTR, {&ddcsz},
"HIDDENA string containing a vector of the relative sizes in the z "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-gcom", FALSE, etINT, {&nstglobalcomm},
"Global communication frequency" },
{ "-nb", FALSE, etENUM, {&nbpu_opt},
"Calculate non-bonded interactions on" },
{ "-nstlist", FALSE, etINT, {&nstlist},
"Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
{ "-tunepme", FALSE, etBOOL, {&bTunePME},
"Optimize PME load between PP/PME ranks or GPU/CPU" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL, {&bReproducible},
"Try to avoid optimizations that affect binary reproducibility" },
{ "-cpt", FALSE, etREAL, {&cpt_period},
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bTryToAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-nsteps", FALSE, etINT64, {&nsteps},
"Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT, {&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
"Attempt replica exchange periodically with this period (steps)" },
{ "-nex", FALSE, etINT, {&repl_ex_nex},
"Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-imdport", FALSE, etINT, {&imdport},
"HIDDENIMD listening port" },
{ "-imdwait", FALSE, etBOOL, {&bIMDwait},
"HIDDENPause the simulation while no IMD client is connected" },
{ "-imdterm", FALSE, etBOOL, {&bIMDterm},
"HIDDENAllow termination of the simulation from IMD client" },
{ "-imdpull", FALSE, etBOOL, {&bIMDpull},
"HIDDENAllow pulling in the simulation from IMD client" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining wall clock time for the run" },
{ "-resetstep", FALSE, etINT, {&resetstep},
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
};
unsigned long Flags;
ivec ddxyz;
int dd_rank_order;
gmx_bool bDoAppendFiles, bStartFromCpt;
FILE *fplog;
int rc;
char **multidir = NULL;
cr = init_commrec();
unsigned long PCA_Flags = PCA_CAN_SET_DEFFNM;
// With -multi or -multidir, the file names are going to get processed
// further (or the working directory changed), so we can't check for their
// existence during parsing. It isn't useful to do any completion based on
// file system contents, either.
if (is_multisim_option_set(argc, argv))
{
PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
}
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
* also comment out the version of init_forcerec in md.c
* with NULL instead of opt2fn
*/
/*
if (!MASTER(cr))
{
PCA_Flags |= PCA_NOT_READ_NODE;
}
*/
if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv))
{
sfree(cr);
return 0;
}
dd_rank_order = nenum(ddrank_opt);
hw_opt.thread_affinity = nenum(thread_aff_opt);
/* now check the -multi and -multidir option */
if (opt2bSet("-multidir", NFILE, fnm))
{
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
}
if (repl_ex_nst != 0 && nmultisim < 2)
{
gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
}
if (repl_ex_nex < 0)
{
gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
}
if (nmultisim >= 1)
{
#if !GMX_THREAD_MPI
init_multisystem(cr, nmultisim, multidir, NFILE, fnm);
#else
gmx_fatal(FARGS, "mdrun -multi or -multidir are not supported with the thread-MPI library. "
"Please compile GROMACS with a proper external MPI library.");
#endif
}
if (!opt2bSet("-cpi", NFILE, fnm))
{
// If we are not starting from a checkpoint we never allow files to be appended
// to, since that has caused a ton of strange behaviour and bugs in the past.
if (opt2parg_bSet("-append", asize(pa), pa))
{
// If the user explicitly used the -append option, explain that it is not possible.
gmx_fatal(FARGS, "GROMACS can only append to files when restarting from a checkpoint.");
}
else
{
// If the user did not say anything explicit, just disable appending.
bTryToAppendFiles = FALSE;
}
}
handleRestart(cr, bTryToAppendFiles, NFILE, fnm, &bDoAppendFiles, &bStartFromCpt);
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
Flags = Flags | (opt2parg_bSet("-ntomp", asize(pa), pa) ? MD_NTOMPSET : 0);
Flags = Flags | (bIMDwait ? MD_IMDWAIT : 0);
Flags = Flags | (bIMDterm ? MD_IMDTERM : 0);
Flags = Flags | (bIMDpull ? MD_IMDPULL : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
if (MASTER(cr) && !bDoAppendFiles)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
Flags & MD_APPENDFILES, &fplog);
}
else
{
fplog = NULL;
}
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
rc = gmx::mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose,
nstglobalcomm, ddxyz, dd_rank_order, npme, rdd, rconstr,
dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
nbpu_opt[0], nstlist,
nsteps, nstepout, resetstep,
nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
pforce, cpt_period, max_hours, imdport, Flags);
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bDoAppendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
int gmx_do_dssp(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] ",
"reads a trajectory file and computes the secondary structure for",
"each time frame ",
"calling the dssp program. If you do not have the dssp program,",
"get it from http://swift.cmbi.ru.nl/gv/dssp. [THISMODULE] assumes ",
"that the dssp executable is located in ",
"[TT]/usr/local/bin/dssp[tt]. If this is not the case, then you should",
"set an environment variable [TT]DSSP[tt] pointing to the dssp",
"executable, e.g.: [PAR]",
"[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]",
"Since version 2.0.0, dssp is invoked with a syntax that differs",
"from earlier versions. If you have an older version of dssp,",
"use the [TT]-ver[tt] option to direct do_dssp to use the older syntax.",
"By default, do_dssp uses the syntax introduced with version 2.0.0.",
"Even newer versions (which at the time of writing are not yet released)",
"are assumed to have the same syntax as 2.0.0.[PAR]",
"The structure assignment for each residue and time is written to an",
"[TT].xpm[tt] matrix file. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [TT]xpm2ps[tt].",
"Individual chains are separated by light grey lines in the [TT].xpm[tt] and",
"postscript files.",
"The number of residues with each secondary structure type and the",
"total secondary structure ([TT]-sss[tt]) count as a function of",
"time are also written to file ([TT]-sc[tt]).[PAR]",
"Solvent accessible surface (SAS) per residue can be calculated, both in",
"absolute values (A^2) and in fractions of the maximal accessible",
"surface of a residue. The maximal accessible surface is defined as",
"the accessible surface of a residue in a chain of glycines.",
"[BB]Note[bb] that the program [gmx-sas] can also compute SAS",
"and that is more efficient.[PAR]",
"Finally, this program can dump the secondary structure in a special file",
"[TT]ssdump.dat[tt] for usage in the program [gmx-chi]. Together",
"these two programs can be used to analyze dihedral properties as a",
"function of secondary structure type."
};
static gmx_bool bVerbose;
static const char *ss_string = "HEBT";
static int dsspVersion = 2;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"HIDDENGenerate miles of useless information" },
{ "-sss", FALSE, etSTR, {&ss_string},
"Secondary structures for structure count"},
{ "-ver", FALSE, etINT, {&dsspVersion},
"DSSP major version. Syntax changed with version 2"}
};
t_trxstatus *status;
FILE *tapein;
FILE *ss, *acc, *fTArea, *tmpf;
const char *fnSCount, *fnArea, *fnTArea, *fnAArea;
const char *leg[] = { "Phobic", "Phylic" };
t_topology top;
int ePBC;
t_atoms *atoms;
t_matrix mat;
int nres, nr0, naccr, nres_plus_separators;
gmx_bool *bPhbres, bDoAccSurf;
real t;
int i, j, natoms, nframe = 0;
matrix box = {{0}};
int gnx;
char *grpnm, *ss_str;
atom_id *index;
rvec *xp, *x;
int *average_area;
real **accr, *accr_ptr = NULL, *av_area, *norm_av_area;
char pdbfile[32], tmpfile[32], title[256];
char dssp[256];
const char *dptr;
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-ssdump", "ssdump", ffOPTWR },
{ efMAP, "-map", "ss", ffLIBRD },
{ efXPM, "-o", "ss", ffWRITE },
{ efXVG, "-sc", "scount", ffWRITE },
{ efXPM, "-a", "area", ffOPTWR },
{ efXVG, "-ta", "totarea", ffOPTWR },
{ efXVG, "-aa", "averarea", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
fnSCount = opt2fn("-sc", NFILE, fnm);
fnArea = opt2fn_null("-a", NFILE, fnm);
fnTArea = opt2fn_null("-ta", NFILE, fnm);
fnAArea = opt2fn_null("-aa", NFILE, fnm);
bDoAccSurf = (fnArea || fnTArea || fnAArea);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xp, NULL, box, FALSE);
atoms = &(top.atoms);
check_oo(atoms);
bPhbres = bPhobics(atoms);
get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpnm);
nres = 0;
nr0 = -1;
for (i = 0; (i < gnx); i++)
{
if (atoms->atom[index[i]].resind != nr0)
{
nr0 = atoms->atom[index[i]].resind;
nres++;
}
}
fprintf(stderr, "There are %d residues in your selected group\n", nres);
strcpy(pdbfile, "ddXXXXXX");
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile, "w")) == NULL)
{
sprintf(pdbfile, "%ctmp%cfilterXXXXXX", DIR_SEPARATOR, DIR_SEPARATOR);
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile, "w")) == NULL)
{
gmx_fatal(FARGS, "Can not open tmp file %s", pdbfile);
}
}
else
{
fclose(tmpf);
}
strcpy(tmpfile, "ddXXXXXX");
gmx_tmpnam(tmpfile);
if ((tmpf = fopen(tmpfile, "w")) == NULL)
{
sprintf(tmpfile, "%ctmp%cfilterXXXXXX", DIR_SEPARATOR, DIR_SEPARATOR);
gmx_tmpnam(tmpfile);
if ((tmpf = fopen(tmpfile, "w")) == NULL)
{
gmx_fatal(FARGS, "Can not open tmp file %s", tmpfile);
}
}
else
{
fclose(tmpf);
}
if ((dptr = getenv("DSSP")) == NULL)
{
dptr = "/usr/local/bin/dssp";
}
if (!gmx_fexist(dptr))
{
gmx_fatal(FARGS, "DSSP executable (%s) does not exist (use setenv DSSP)",
dptr);
}
if (dsspVersion >= 2)
{
if (dsspVersion > 2)
{
printf("\nWARNING: You use DSSP version %d, which is not explicitly\nsupported by do_dssp. Assuming version 2 syntax.\n\n", dsspVersion);
}
sprintf(dssp, "%s -i %s -o %s > /dev/null %s",
dptr, pdbfile, tmpfile, bVerbose ? "" : "2> /dev/null");
}
else
{
sprintf(dssp, "%s %s %s %s > /dev/null %s",
dptr, bDoAccSurf ? "" : "-na", pdbfile, tmpfile, bVerbose ? "" : "2> /dev/null");
}
fprintf(stderr, "dssp cmd='%s'\n", dssp);
if (fnTArea)
{
fTArea = xvgropen(fnTArea, "Solvent Accessible Surface Area",
output_env_get_xvgr_tlabel(oenv), "Area (nm\\S2\\N)", oenv);
xvgr_legend(fTArea, 2, leg, oenv);
}
else
{
fTArea = NULL;
}
mat.map = NULL;
mat.nmap = readcmap(opt2fn("-map", NFILE, fnm), &(mat.map));
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
if (natoms > atoms->nr)
{
gmx_fatal(FARGS, "\nTrajectory does not match topology!");
}
if (gnx > natoms)
{
gmx_fatal(FARGS, "\nTrajectory does not match selected group!");
}
snew(average_area, atoms->nres);
snew(av_area, atoms->nres);
snew(norm_av_area, atoms->nres);
accr = NULL;
naccr = 0;
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
do
{
t = output_env_conv_time(oenv, t);
if (bDoAccSurf && nframe >= naccr)
{
naccr += 10;
srenew(accr, naccr);
for (i = naccr-10; i < naccr; i++)
{
snew(accr[i], 2*atoms->nres-1);
}
}
gmx_rmpbc(gpbc, natoms, box, x);
tapein = gmx_ffopen(pdbfile, "w");
write_pdbfile_indexed(tapein, NULL, atoms, x, ePBC, box, ' ', -1, gnx, index, NULL, TRUE);
gmx_ffclose(tapein);
if (0 != system(dssp))
{
gmx_fatal(FARGS, "Failed to execute command: %s\n",
"Try specifying your dssp version with the -ver option.", dssp);
}
/* strip_dssp returns the number of lines found in the dssp file, i.e.
* the number of residues plus the separator lines */
if (bDoAccSurf)
{
accr_ptr = accr[nframe];
}
nres_plus_separators = strip_dssp(tmpfile, nres, bPhbres, t,
accr_ptr, fTArea, &mat, average_area, oenv);
remove(tmpfile);
remove(pdbfile);
nframe++;
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
close_trj(status);
if (fTArea)
{
xvgrclose(fTArea);
}
gmx_rmpbc_done(gpbc);
prune_ss_legend(&mat);
ss = opt2FILE("-o", NFILE, fnm, "w");
mat.flags = 0;
write_xpm_m(ss, mat);
gmx_ffclose(ss);
if (opt2bSet("-ssdump", NFILE, fnm))
{
ss = opt2FILE("-ssdump", NFILE, fnm, "w");
snew(ss_str, nres+1);
fprintf(ss, "%d\n", nres);
for (j = 0; j < mat.nx; j++)
{
for (i = 0; (i < mat.ny); i++)
{
ss_str[i] = mat.map[mat.matrix[j][i]].code.c1;
}
ss_str[i] = '\0';
fprintf(ss, "%s\n", ss_str);
}
gmx_ffclose(ss);
sfree(ss_str);
}
analyse_ss(fnSCount, &mat, ss_string, oenv);
if (bDoAccSurf)
{
write_sas_mat(fnArea, accr, nframe, nres_plus_separators, &mat);
for (i = 0; i < atoms->nres; i++)
{
av_area[i] = (average_area[i] / (real)nframe);
}
norm_acc(atoms, nres, av_area, norm_av_area);
if (fnAArea)
{
acc = xvgropen(fnAArea, "Average Accessible Area",
"Residue", "A\\S2", oenv);
for (i = 0; (i < nres); i++)
{
fprintf(acc, "%5d %10g %10g\n", i+1, av_area[i], norm_av_area[i]);
}
xvgrclose(acc);
}
}
view_all(oenv, NFILE, fnm);
return 0;
}
int gmx_editconf(int argc, char *argv[])
{
const char
*desc[] =
{
"editconf converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
"or [TT].pdb[tt].",
"[PAR]",
"The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
"[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
"will center the system in the box, unless [TT]-noc[tt] is used.",
"[PAR]",
"Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
"triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
"[TT]dodecahedron[tt] represents a rhombic dodecahedron and",
"[TT]octahedron[tt] is a truncated octahedron.",
"The last two are special cases of a triclinic box.",
"The length of the three box vectors of the truncated octahedron is the",
"shortest distance between two opposite hexagons.",
"The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
"is 0.77 of that of a cubic box with the same periodic image distance.",
"[PAR]",
"Option [TT]-box[tt] requires only",
"one value for a cubic box, dodecahedron and a truncated octahedron.",
"[PAR]",
"With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
"and z directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
"[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
"to the diameter of the system (largest distance between atoms) plus twice",
"the specified distance.",
"[PAR]",
"Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
"a triclinic box and can not be used with option [TT]-d[tt].",
"[PAR]",
"When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
"can be selected for calculating the size and the geometric center,",
"otherwise the whole system is used.",
"[PAR]",
"[TT]-rotate[tt] rotates the coordinates and velocities.",
"[PAR]",
"[TT]-princ[tt] aligns the principal axes of the system along the",
"coordinate axes, this may allow you to decrease the box volume,",
"but beware that molecules can rotate significantly in a nanosecond.",
"[PAR]",
"Scaling is applied before any of the other operations are",
"performed. Boxes and coordinates can be scaled to give a certain density (option",
"[TT]-density[tt]). Note that this may be inaccurate in case a gro",
"file is given as input. A special feature of the scaling option, when the",
"factor -1 is given in one dimension, one obtains a mirror image,",
"mirrored in one of the plains, when one uses -1 in three dimensions",
"a point-mirror image is obtained.[PAR]",
"Groups are selected after all operations have been applied.[PAR]",
"Periodicity can be removed in a crude manner.",
"It is important that the box sizes at the bottom of your input file",
"are correct when the periodicity is to be removed.",
"[PAR]",
"When writing [TT].pdb[tt] files, B-factors can be",
"added with the [TT]-bf[tt] option. B-factors are read",
"from a file with with following format: first line states number of",
"entries in the file, next lines state an index",
"followed by a B-factor. The B-factors will be attached per residue",
"unless an index is larger than the number of residues or unless the",
"[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
"be added instead of B-factors. [TT]-legend[tt] will produce",
"a row of CA atoms with B-factors ranging from the minimum to the",
"maximum value found, effectively making a legend for viewing.",
"[PAR]",
"With the option -mead a special pdb (pqr) file for the MEAD electrostatics",
"program (Poisson-Boltzmann solver) can be made. A further prerequisite",
"is that the input file is a run input file.",
"The B-factor field is then filled with the Van der Waals radius",
"of the atoms while the occupancy field will hold the charge.",
"[PAR]",
"The option -grasp is similar, but it puts the charges in the B-factor",
"and the radius in the occupancy.",
"[PAR]",
"Option [TT]-align[tt] allows alignment",
"of the principal axis of a specified group against the given vector, ",
"with an optional center of rotation specified by [TT]-aligncenter[tt].",
"[PAR]",
"Finally with option [TT]-label[tt] editconf can add a chain identifier",
"to a pdb file, which can be useful for analysis with e.g. rasmol.",
"[PAR]",
"To convert a truncated octrahedron file produced by a package which uses",
"a cubic box with the corners cut off (such as Gromos) use:[BR]",
"[TT]editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out>[tt][BR]",
"where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2." };
const char *bugs[] =
{
"For complex molecules, the periodicity removal routine may break down, ",
"in that case you can use trjconv." };
static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
FALSE, bCONECT = FALSE;
static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
FALSE, bGrasp = FALSE, bSig56 = FALSE;
static rvec scale =
{ 1, 1, 1 }, newbox =
{ 0, 0, 0 }, newang =
{ 90, 90, 90 };
static real rho = 1000.0, rvdw = 0.12;
static rvec center =
{ 0, 0, 0 }, translation =
{ 0, 0, 0 }, rotangles =
{ 0, 0, 0 }, aligncenter =
{ 0, 0, 0 }, targetvec =
{ 0, 0, 0 };
static const char *btype[] =
{ NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },
*label = "A";
static rvec visbox =
{ 0, 0, 0 };
t_pargs
pa[] =
{
{ "-ndef", FALSE, etBOOL,
{ &bNDEF }, "Choose output from default index groups" },
{ "-visbox", FALSE, etRVEC,
{ visbox },
"HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
{ "-bt", FALSE, etENUM,
{ btype }, "Box type for -box and -d" },
{ "-box", FALSE, etRVEC,
{ newbox }, "Box vector lengths (a,b,c)" },
{ "-angles", FALSE, etRVEC,
{ newang }, "Angles between the box vectors (bc,ac,ab)" },
{ "-d", FALSE, etREAL,
{ &dist }, "Distance between the solute and the box" },
{ "-c", FALSE, etBOOL,
{ &bCenter },
"Center molecule in box (implied by -box and -d)" },
{ "-center", FALSE, etRVEC,
{ center }, "Coordinates of geometrical center" },
{ "-aligncenter", FALSE, etRVEC,
{ aligncenter }, "Center of rotation for alignment" },
{ "-align", FALSE, etRVEC,
{ targetvec },
"Align to target vector" },
{ "-translate", FALSE, etRVEC,
{ translation }, "Translation" },
{ "-rotate", FALSE, etRVEC,
{ rotangles },
"Rotation around the X, Y and Z axes in degrees" },
{ "-princ", FALSE, etBOOL,
{ &bOrient },
"Orient molecule(s) along their principal axes" },
{ "-scale", FALSE, etRVEC,
{ scale }, "Scaling factor" },
{ "-density", FALSE, etREAL,
{ &rho },
"Density (g/l) of the output box achieved by scaling" },
{ "-pbc", FALSE, etBOOL,
{ &bRMPBC },
"Remove the periodicity (make molecule whole again)" },
{ "-grasp", FALSE, etBOOL,
{ &bGrasp },
"Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
{
"-rvdw", FALSE, etREAL,
{ &rvdw },
"Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file" },
{ "-sig56", FALSE, etREAL,
{ &bSig56 },
"Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 " },
{
"-vdwread", FALSE, etBOOL,
{ &bReadVDW },
"Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field" },
{ "-atom", FALSE, etBOOL,
{ &peratom }, "Force B-factor attachment per atom" },
{ "-legend", FALSE, etBOOL,
{ &bLegend }, "Make B-factor legend" },
{ "-label", FALSE, etSTR,
{ &label }, "Add chain label for all residues" },
{
"-conect", FALSE, etBOOL,
{ &bCONECT },
"Add CONECT records to a pdb file when written. Can only be done when a topology is present" } };
#define NPA asize(pa)
FILE *out;
const char *infile, *outfile;
char title[STRLEN];
int outftp, inftp, natom, i, j, n_bfac, itype, ntype;
double *bfac = NULL, c6, c12;
int *bfac_nr = NULL;
t_topology *top = NULL;
t_atoms atoms;
char *grpname, *sgrpname, *agrpname;
int isize, ssize, tsize, asize;
atom_id *index, *sindex, *tindex, *aindex;
rvec *x, *v, gc, min, max, size;
int ePBC;
matrix box,rotmatrix,trans;
rvec princd,tmpvec;
gmx_bool bIndex, bSetSize, bSetAng, bCubic, bDist, bSetCenter, bAlign;
gmx_bool bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
real xs, ys, zs, xcent, ycent, zcent, diam = 0, mass = 0, d, vdw;
gmx_atomprop_t aps;
gmx_conect conect;
output_env_t oenv;
t_filenm fnm[] =
{
{ efSTX, "-f", NULL, ffREAD },
{ efNDX, "-n", NULL, ffOPTRD },
{ efSTO, NULL, NULL, ffOPTWR },
{ efPQR, "-mead", "mead", ffOPTWR },
{ efDAT, "-bf", "bfact", ffOPTRD } };
#define NFILE asize(fnm)
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
bMead = opt2bSet("-mead", NFILE, fnm);
bSetSize = opt2parg_bSet("-box", NPA, pa);
bSetAng = opt2parg_bSet("-angles", NPA, pa);
bSetCenter = opt2parg_bSet("-center", NPA, pa);
bDist = opt2parg_bSet("-d", NPA, pa);
bAlign = opt2parg_bSet("-align", NPA, pa);
/* Only automatically turn on centering without -noc */
if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c", NPA, pa))
{
bCenter = TRUE;
}
bScale = opt2parg_bSet("-scale", NPA, pa);
bRho = opt2parg_bSet("-density", NPA, pa);
bTranslate = opt2parg_bSet("-translate", NPA, pa);
bRotate = opt2parg_bSet("-rotate", NPA, pa);
if (bScale && bRho)
fprintf(stderr, "WARNING: setting -density overrides -scale\n");
bScale = bScale || bRho;
bCalcGeom = bCenter || bRotate || bOrient || bScale;
bCalcDiam = btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o';
infile = ftp2fn(efSTX, NFILE, fnm);
if (bMead)
outfile = ftp2fn(efPQR, NFILE, fnm);
else
outfile = ftp2fn(efSTO, NFILE, fnm);
outftp = fn2ftp(outfile);
inftp = fn2ftp(infile);
aps = gmx_atomprop_init();
if (bMead && bGrasp)
{
printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
bGrasp = FALSE;
}
if (bGrasp && (outftp != efPDB))
gmx_fatal(FARGS, "Output file should be a .pdb file"
" when using the -grasp option\n");
if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
(fn2ftp(infile) == efTPA) ||
(fn2ftp(infile) == efTPB)))
gmx_fatal(FARGS,"Input file should be a .tp[abr] file"
" when using the -mead option\n");
get_stx_coordnum(infile,&natom);
init_t_atoms(&atoms,natom,TRUE);
snew(x,natom);
snew(v,natom);
read_stx_conf(infile,title,&atoms,x,v,&ePBC,box);
if (fn2ftp(infile) == efPDB)
{
get_pdb_atomnumber(&atoms,aps);
}
printf("Read %d atoms\n",atoms.nr);
/* Get the element numbers if available in a pdb file */
if (fn2ftp(infile) == efPDB)
get_pdb_atomnumber(&atoms,aps);
if (ePBC != epbcNONE)
{
real vol = det(box);
printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
vol,100*((int)(vol*4.5)));
}
if (bMead || bGrasp || bCONECT)
top = read_top(infile,NULL);
if (bMead || bGrasp)
{
if (atoms.nr != top->atoms.nr)
gmx_fatal(FARGS,"Atom numbers don't match (%d vs. %d)",atoms.nr,top->atoms.nr);
snew(atoms.pdbinfo,top->atoms.nr);
ntype = top->idef.atnr;
for(i=0; (i<atoms.nr); i++) {
/* Determine the Van der Waals radius from the force field */
if (bReadVDW) {
if (!gmx_atomprop_query(aps,epropVDW,
*top->atoms.resinfo[top->atoms.atom[i].resind].name,
*top->atoms.atomname[i],&vdw))
vdw = rvdw;
}
else {
itype = top->atoms.atom[i].type;
c12 = top->idef.iparams[itype*ntype+itype].lj.c12;
c6 = top->idef.iparams[itype*ntype+itype].lj.c6;
if ((c6 != 0) && (c12 != 0)) {
real sig6;
if (bSig56)
sig6 = 2*c12/c6;
else
sig6 = c12/c6;
vdw = 0.5*pow(sig6,1.0/6.0);
}
else
vdw = rvdw;
}
/* Factor of 10 for nm -> Angstroms */
vdw *= 10;
if (bMead) {
atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
atoms.pdbinfo[i].bfac = vdw;
}
else {
atoms.pdbinfo[i].occup = vdw;
atoms.pdbinfo[i].bfac = top->atoms.atom[i].q;
}
}
}
bHaveV=FALSE;
for (i=0; (i<natom) && !bHaveV; i++)
for (j=0; (j<DIM) && !bHaveV; j++)
bHaveV=bHaveV || (v[i][j]!=0);
printf("%selocities found\n",bHaveV?"V":"No v");
if (visbox[0] > 0) {
if (bIndex)
gmx_fatal(FARGS,"Sorry, can not visualize box with index groups");
if (outftp != efPDB)
gmx_fatal(FARGS,"Sorry, can only visualize box with a pdb file");
} else if (visbox[0] == -1)
visualize_images("images.pdb",ePBC,box);
/* remove pbc */
if (bRMPBC)
rm_gropbc(&atoms,x,box);
if (bCalcGeom) {
if (bIndex) {
fprintf(stderr,"\nSelect a group for determining the system size:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
diam=calc_geom(ssize,sindex,x,gc,min,max,bCalcDiam);
rvec_sub(max, min, size);
printf(" system size :%7.3f%7.3f%7.3f (nm)\n",
size[XX], size[YY], size[ZZ]);
if (bCalcDiam)
printf(" diameter :%7.3f (nm)\n",diam);
printf(" center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf(" box volume :%7.2f (nm^3)\n",det(box));
}
if (bRho || bOrient || bAlign)
mass = calc_mass(&atoms,!fn2bTPX(infile),aps);
if (bOrient) {
atom_id *index;
char *grpnames;
/* Get a group for principal component analysis */
fprintf(stderr,"\nSelect group for the determining the orientation\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpnames);
/* Orient the principal axes along the coordinate axes */
orient_princ(&atoms,isize,index,natom,x,bHaveV ? v : NULL, NULL);
sfree(index);
sfree(grpnames);
}
if ( bScale ) {
/* scale coordinates and box */
if (bRho) {
/* Compute scaling constant */
real vol,dens;
vol = det(box);
dens = (mass*AMU)/(vol*NANO*NANO*NANO);
fprintf(stderr,"Volume of input %g (nm^3)\n",vol);
fprintf(stderr,"Mass of input %g (a.m.u.)\n",mass);
fprintf(stderr,"Density of input %g (g/l)\n",dens);
if (vol==0 || mass==0)
gmx_fatal(FARGS,"Cannot scale density with "
"zero mass (%g) or volume (%g)\n",mass,vol);
scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho,1.0/3.0);
fprintf(stderr,"Scaling all box vectors by %g\n",scale[XX]);
}
scale_conf(atoms.nr,x,box,scale);
}
if (bAlign) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to align:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&asize,&aindex,&agrpname);
} else {
asize = atoms.nr;
snew(aindex,asize);
for (i=0;i<asize;i++)
aindex[i]=i;
}
printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n",asize,natom,
targetvec[XX],targetvec[YY],targetvec[ZZ],
aligncenter[XX],aligncenter[YY],aligncenter[ZZ]);
/*subtract out pivot point*/
for(i=0; i<asize; i++)
rvec_dec(x[aindex[i]],aligncenter);
/*now determine transform and rotate*/
/*will this work?*/
principal_comp(asize,aindex,atoms.atom,x, trans,princd);
unitv(targetvec,targetvec);
printf("Using %g %g %g as principal axis\n", trans[0][2],trans[1][2],trans[2][2]);
tmpvec[XX]=trans[0][2]; tmpvec[YY]=trans[1][2]; tmpvec[ZZ]=trans[2][2];
calc_rotmatrix(tmpvec, targetvec, rotmatrix);
/* rotmatrix finished */
for (i=0;i<asize;++i)
{
mvmul(rotmatrix,x[aindex[i]],tmpvec);
copy_rvec(tmpvec,x[aindex[i]]);
}
/*add pivot point back*/
for(i=0; i<asize; i++)
rvec_inc(x[aindex[i]],aligncenter);
if (!bIndex)
sfree(aindex);
}
if (bTranslate) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to translate:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
printf("Translating %d atoms (out of %d) by %g %g %g nm\n",ssize,natom,
translation[XX],translation[YY],translation[ZZ]);
if (sindex) {
for(i=0; i<ssize; i++)
rvec_inc(x[sindex[i]],translation);
}
else {
for(i=0; i<natom; i++)
rvec_inc(x[i],translation);
}
}
if (bRotate) {
/* Rotate */
printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n",rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<DIM; i++)
rotangles[i] *= DEG2RAD;
rotate_conf(natom,x,v,rotangles[XX],rotangles[YY],rotangles[ZZ]);
}
if (bCalcGeom) {
/* recalc geometrical center and max and min coordinates and size */
calc_geom(ssize,sindex,x,gc,min,max,FALSE);
rvec_sub(max, min, size);
if (bScale || bOrient || bRotate)
printf("new system size : %6.3f %6.3f %6.3f\n",
size[XX],size[YY],size[ZZ]);
}
if (bSetSize || bDist || (btype[0][0]=='t' && bSetAng)) {
ePBC = epbcXYZ;
if (!(bSetSize || bDist))
for (i=0; i<DIM; i++)
newbox[i] = norm(box[i]);
clear_mat(box);
/* calculate new boxsize */
switch(btype[0][0]){
case 't':
if (bDist)
for(i=0; i<DIM; i++)
newbox[i] = size[i]+2*dist;
if (!bSetAng) {
box[XX][XX] = newbox[XX];
box[YY][YY] = newbox[YY];
box[ZZ][ZZ] = newbox[ZZ];
} else {
matrix_convert(box,newbox,newang);
}
break;
case 'c':
case 'd':
case 'o':
if (bSetSize)
d = newbox[0];
else
d = diam+2*dist;
if (btype[0][0] == 'c')
for(i=0; i<DIM; i++)
box[i][i] = d;
else if (btype[0][0] == 'd') {
box[XX][XX] = d;
box[YY][YY] = d;
box[ZZ][XX] = d/2;
box[ZZ][YY] = d/2;
box[ZZ][ZZ] = d*sqrt(2)/2;
} else {
box[XX][XX] = d;
box[YY][XX] = d/3;
box[YY][YY] = d*sqrt(2)*2/3;
box[ZZ][XX] = -d/3;
box[ZZ][YY] = d*sqrt(2)/3;
box[ZZ][ZZ] = d*sqrt(6)/3;
}
break;
}
}
/* calculate new coords for geometrical center */
if (!bSetCenter)
calc_box_center(ecenterDEF,box,center);
/* center molecule on 'center' */
if (bCenter)
center_conf(natom,x,center,gc);
/* print some */
if (bCalcGeom) {
calc_geom(ssize,sindex,x, gc, min, max, FALSE);
printf("new center :%7.3f%7.3f%7.3f (nm)\n",gc[XX],gc[YY],gc[ZZ]);
}
if (bOrient || bScale || bDist || bSetSize) {
printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf("new box volume :%7.2f (nm^3)\n",det(box));
}
if (check_box(epbcXYZ,box))
printf("\nWARNING: %s\n",check_box(epbcXYZ,box));
if (bDist && btype[0][0]=='t')
{
if(TRICLINIC(box))
{
printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
"distance from the solute to a box surface along the corresponding normal\n"
"vector might be somewhat smaller than your specified value %f.\n"
"You can check the actual value with g_mindist -pi\n",dist);
}
else
{
printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
"If the molecule rotates the actual distance will be smaller. You might want\n"
"to use a cubic box instead, or why not try a dodecahedron today?\n");
}
}
if (bCONECT && (outftp == efPDB) && (inftp == efTPR))
conect = gmx_conect_generate(top);
else
conect = NULL;
if (bIndex) {
fprintf(stderr,"\nSelect a group for output:\n");
get_index(&atoms,opt2fn_null("-n",NFILE,fnm),
1,&isize,&index,&grpname);
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
if (opt2bSet("-bf",NFILE,fnm) || bLegend)
{
gmx_fatal(FARGS,"Sorry, cannot do bfactors with an index group.");
}
if (outftp == efPDB)
{
out=ffopen(outfile,"w");
write_pdbfile_indexed(out,title,&atoms,x,ePBC,box,' ',1,isize,index,conect,TRUE);
ffclose(out);
}
else
{
write_sto_conf_indexed(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box,isize,index);
}
}
else {
if ((outftp == efPDB) || (outftp == efPQR)) {
out=ffopen(outfile,"w");
if (bMead) {
set_pdb_wide_format(TRUE);
fprintf(out,"REMARK "
"The B-factors in this file hold atomic radii\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic charges\n");
}
else if (bGrasp) {
fprintf(out,"GRASP PDB FILE\nFORMAT NUMBER=1\n");
fprintf(out,"REMARK "
"The B-factors in this file hold atomic charges\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic radii\n");
}
else if (opt2bSet("-bf",NFILE,fnm)) {
read_bfac(opt2fn("-bf",NFILE,fnm),&n_bfac,&bfac,&bfac_nr);
set_pdb_conf_bfac(atoms.nr,atoms.nres,&atoms,
n_bfac,bfac,bfac_nr,peratom);
}
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
write_pdbfile(out,title,&atoms,x,ePBC,box,' ',-1,conect,TRUE);
if (bLegend)
pdb_legend(out,atoms.nr,atoms.nres,&atoms,x);
if (visbox[0] > 0)
visualize_box(out,bLegend ? atoms.nr+12 : atoms.nr,
bLegend? atoms.nres=12 : atoms.nres,box,visbox);
ffclose(out);
}
else
write_sto_conf(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box);
}
gmx_atomprop_destroy(aps);
do_view(oenv,outfile,NULL);
thanx(stderr);
return 0;
}
int gmx_x2top(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] generates a primitive topology from a coordinate file.",
"The program assumes all hydrogens are present when defining",
"the hybridization from the atom name and the number of bonds.",
"The program can also make an [TT].rtp[tt] entry, which you can then add",
"to the [TT].rtp[tt] database.[PAR]",
"When [TT]-param[tt] is set, equilibrium distances and angles",
"and force constants will be printed in the topology for all",
"interactions. The equilibrium distances and angles are taken",
"from the input coordinates, the force constant are set with",
"command line options.",
"The force fields somewhat supported currently are:[PAR]",
"G53a5 GROMOS96 53a5 Forcefield (official distribution)[PAR]",
"oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)[PAR]",
"The corresponding data files can be found in the library directory",
"with name [TT]atomname2type.n2t[tt]. Check Chapter 5 of the manual for more",
"information about file formats. By default, the force field selection",
"is interactive, but you can use the [TT]-ff[tt] option to specify",
"one of the short names above on the command line instead. In that",
"case [THISMODULE] just looks for the corresponding file.[PAR]",
};
const char *bugs[] = {
"The atom type selection is primitive. Virtually no chemical knowledge is used",
"Periodic boundary conditions screw up the bonding",
"No improper dihedrals are generated",
"The atoms to atomtype translation table is incomplete ([TT]atomname2type.n2t[tt] file in the data directory). Please extend it and send the results back to the GROMACS crew."
};
FILE *fp;
t_params plist[F_NRE];
t_excls *excls;
t_atoms *atoms; /* list with all atoms */
gpp_atomtype_t atype;
t_nextnb nnb;
t_nm2type *nm2t;
t_mols mymol;
int nnm;
char title[STRLEN], forcefield[32], ffdir[STRLEN];
rvec *x; /* coordinates? */
int *nbonds, *cgnr;
int bts[] = { 1, 1, 1, 2 };
matrix box; /* box length matrix */
int natoms; /* number of atoms in one molecule */
int nres; /* number of molecules? */
int i, j, k, l, m, ndih;
int epbc;
gmx_bool bRTP, bTOP, bOPLS;
t_symtab symtab;
real cutoff, qtot, mtot;
char n2t[STRLEN];
output_env_t oenv;
t_filenm fnm[] = {
{ efSTX, "-f", "conf", ffREAD },
{ efTOP, "-o", "out", ffOPTWR },
{ efRTP, "-r", "out", ffOPTWR }
};
#define NFILE asize(fnm)
static real scale = 1.1, kb = 4e5, kt = 400, kp = 5;
static t_restp rtp_header_settings;
static gmx_bool bRemoveDihedralIfWithImproper = FALSE;
static gmx_bool bGenerateHH14Interactions = TRUE;
static gmx_bool bKeepAllGeneratedDihedrals = FALSE;
static int nrexcl = 3;
static gmx_bool bParam = TRUE, bRound = TRUE;
static gmx_bool bPairs = TRUE, bPBC = TRUE;
static gmx_bool bUsePDBcharge = FALSE, bVerbose = FALSE;
static const char *molnm = "ICE";
static const char *ff = "oplsaa";
t_pargs pa[] = {
{ "-ff", FALSE, etSTR, {&ff},
"Force field for your simulation. Type \"select\" for interactive selection." },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Generate verbose output in the top file." },
{ "-nexcl", FALSE, etINT, {&nrexcl},
"Number of exclusions" },
{ "-H14", FALSE, etBOOL, {&bGenerateHH14Interactions},
"Use 3rd neighbour interactions for hydrogen atoms" },
{ "-alldih", FALSE, etBOOL, {&bKeepAllGeneratedDihedrals},
"Generate all proper dihedrals" },
{ "-remdih", FALSE, etBOOL, {&bRemoveDihedralIfWithImproper},
"Remove dihedrals on the same bond as an improper" },
{ "-pairs", FALSE, etBOOL, {&bPairs},
"Output 1-4 interactions (pairs) in topology file" },
{ "-name", FALSE, etSTR, {&molnm},
"Name of your molecule" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions." },
{ "-pdbq", FALSE, etBOOL, {&bUsePDBcharge},
"Use the B-factor supplied in a [TT].pdb[tt] file for the atomic charges" },
{ "-param", FALSE, etBOOL, {&bParam},
"Print parameters in the output" },
{ "-round", FALSE, etBOOL, {&bRound},
"Round off measured values" },
{ "-kb", FALSE, etREAL, {&kb},
"Bonded force constant (kJ/mol/nm^2)" },
{ "-kt", FALSE, etREAL, {&kt},
"Angle force constant (kJ/mol/rad^2)" },
{ "-kp", FALSE, etREAL, {&kp},
"Dihedral angle force constant (kJ/mol/rad^2)" }
};
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
bRTP = opt2bSet("-r", NFILE, fnm);
bTOP = opt2bSet("-o", NFILE, fnm);
/* C89 requirements mean that these struct members cannot be used in
* the declaration of pa. So some temporary variables are needed. */
rtp_header_settings.bRemoveDihedralIfWithImproper = bRemoveDihedralIfWithImproper;
rtp_header_settings.bGenerateHH14Interactions = bGenerateHH14Interactions;
rtp_header_settings.bKeepAllGeneratedDihedrals = bKeepAllGeneratedDihedrals;
rtp_header_settings.nrexcl = nrexcl;
if (!bRTP && !bTOP)
{
gmx_fatal(FARGS, "Specify at least one output file");
}
/* Force field selection, interactive or direct */
choose_ff(strcmp(ff, "select") == 0 ? NULL : ff,
forcefield, sizeof(forcefield),
ffdir, sizeof(ffdir));
bOPLS = (strcmp(forcefield, "oplsaa") == 0);
mymol.name = strdup(molnm);
mymol.nr = 1;
/* Init parameter lists */
init_plist(plist);
/* Read coordinates */
get_stx_coordnum(opt2fn("-f", NFILE, fnm), &natoms);
snew(atoms, 1);
/* make space for all the atoms */
init_t_atoms(atoms, natoms, TRUE);
snew(x, natoms);
read_stx_conf(opt2fn("-f", NFILE, fnm), title, atoms, x, NULL, &epbc, box);
sprintf(n2t, "%s", ffdir);
nm2t = rd_nm2type(n2t, &nnm);
if (nnm == 0)
{
gmx_fatal(FARGS, "No or incorrect atomname2type.n2t file found (looking for %s)",
n2t);
}
else
{
printf("There are %d name to type translations in file %s\n", nnm, n2t);
}
if (debug)
{
dump_nm2type(debug, nnm, nm2t);
}
printf("Generating bonds from distances...\n");
snew(nbonds, atoms->nr);
mk_bonds(nnm, nm2t, atoms, x, &(plist[F_BONDS]), nbonds, bPBC, box);
open_symtab(&symtab);
atype = set_atom_type(&symtab, atoms, &(plist[F_BONDS]), nbonds, nnm, nm2t);
/* Make Angles and Dihedrals */
snew(excls, atoms->nr);
printf("Generating angles and dihedrals from bonds...\n");
init_nnb(&nnb, atoms->nr, 4);
gen_nnb(&nnb, plist);
print_nnb(&nnb, "NNB");
gen_pad(&nnb, atoms, &rtp_header_settings, plist, excls, NULL, TRUE);
done_nnb(&nnb);
if (!bPairs)
{
plist[F_LJ14].nr = 0;
}
fprintf(stderr,
"There are %4d %s dihedrals, %4d impropers, %4d angles\n"
" %4d pairs, %4d bonds and %4d atoms\n",
plist[F_PDIHS].nr,
bOPLS ? "Ryckaert-Bellemans" : "proper",
plist[F_IDIHS].nr, plist[F_ANGLES].nr,
plist[F_LJ14].nr, plist[F_BONDS].nr, atoms->nr);
calc_angles_dihs(&plist[F_ANGLES], &plist[F_PDIHS], x, bPBC, box);
set_force_const(plist, kb, kt, kp, bRound, bParam);
cgnr = set_cgnr(atoms, bUsePDBcharge, &qtot, &mtot);
printf("Total charge is %g, total mass is %g\n", qtot, mtot);
if (bOPLS)
{
bts[2] = 3;
bts[3] = 1;
}
if (bTOP)
{
fp = ftp2FILE(efTOP, NFILE, fnm, "w");
print_top_header(fp, ftp2fn(efTOP, NFILE, fnm), TRUE, ffdir, 1.0);
write_top(fp, NULL, mymol.name, atoms, FALSE, bts, plist, excls, atype,
cgnr, rtp_header_settings.nrexcl);
print_top_mols(fp, mymol.name, ffdir, NULL, 0, NULL, 1, &mymol);
ffclose(fp);
}
if (bRTP)
{
print_rtp(ftp2fn(efRTP, NFILE, fnm), "Generated by x2top",
atoms, plist, atype, cgnr);
}
if (debug)
{
dump_hybridization(debug, atoms, nbonds);
}
close_symtab(&symtab);
free(mymol.name);
printf("\nWARNING: topologies generated by %s can not be trusted at face value.\n",
ShortProgram());
printf(" Please verify atomtypes and charges by comparison to other\n");
printf(" topologies.\n");
return 0;
}
gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
int mdrun_flags, const t_commrec *cr,
const t_inputrec *ir, gmx_mtop_t *top_global,
const gmx_output_env_t *oenv, gmx_wallcycle_t wcycle)
{
gmx_mdoutf_t of;
char filemode[3];
gmx_bool bAppendFiles, bCiteTng = FALSE;
int i;
snew(of, 1);
of->fp_trn = NULL;
of->fp_ene = NULL;
of->fp_xtc = NULL;
of->tng = NULL;
of->tng_low_prec = NULL;
of->fp_dhdl = NULL;
of->fp_field = NULL;
of->eIntegrator = ir->eI;
of->bExpanded = ir->bExpanded;
of->elamstats = ir->expandedvals->elamstats;
of->simulation_part = ir->simulation_part;
of->x_compression_precision = static_cast<int>(ir->x_compression_precision);
of->wcycle = wcycle;
if (MASTER(cr))
{
bAppendFiles = (mdrun_flags & MD_APPENDFILES);
of->bKeepAndNumCPT = (mdrun_flags & MD_KEEPANDNUMCPT);
sprintf(filemode, bAppendFiles ? "a+" : "w+");
if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
#ifndef GMX_FAHCORE
&&
!(EI_DYNAMICS(ir->eI) &&
ir->nstxout == 0 &&
ir->nstvout == 0 &&
ir->nstfout == 0)
#endif
)
{
const char *filename;
filename = ftp2fn(efTRN, nfile, fnm);
switch (fn2ftp(filename))
{
case efTRR:
case efTRN:
of->fp_trn = gmx_trr_open(filename, filemode);
break;
case efTNG:
gmx_tng_open(filename, filemode[0], &of->tng);
if (filemode[0] == 'w')
{
gmx_tng_prepare_md_writing(of->tng, top_global, ir);
}
bCiteTng = TRUE;
break;
default:
gmx_incons("Invalid full precision file format");
}
}
if (EI_DYNAMICS(ir->eI) &&
ir->nstxout_compressed > 0)
{
const char *filename;
filename = ftp2fn(efCOMPRESSED, nfile, fnm);
switch (fn2ftp(filename))
{
case efXTC:
of->fp_xtc = open_xtc(filename, filemode);
break;
case efTNG:
gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
if (filemode[0] == 'w')
{
gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
}
bCiteTng = TRUE;
break;
default:
gmx_incons("Invalid reduced precision file format");
}
}
if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
{
of->fp_ene = open_enx(ftp2fn(efEDR, nfile, fnm), filemode);
}
of->fn_cpt = opt2fn("-cpo", nfile, fnm);
if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0 &&
(ir->fepvals->separate_dhdl_file == esepdhdlfileYES ) &&
EI_DYNAMICS(ir->eI))
{
if (bAppendFiles)
{
of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl", nfile, fnm), filemode);
}
else
{
of->fp_dhdl = open_dhdl(opt2fn("-dhdl", nfile, fnm), ir, oenv);
}
}
if (opt2bSet("-field", nfile, fnm) &&
(ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
{
if (bAppendFiles)
{
of->fp_field = gmx_fio_fopen(opt2fn("-field", nfile, fnm),
filemode);
}
else
{
of->fp_field = xvgropen(opt2fn("-field", nfile, fnm),
"Applied electric field", "Time (ps)",
"E (V/nm)", oenv);
}
}
/* Set up atom counts so they can be passed to actual
trajectory-writing routines later. Also, XTC writing needs
to know what (and how many) atoms might be in the XTC
groups, and how to look up later which ones they are. */
of->natoms_global = top_global->natoms;
of->groups = &top_global->groups;
of->natoms_x_compressed = 0;
for (i = 0; (i < top_global->natoms); i++)
{
if (ggrpnr(of->groups, egcCompressedX, i) == 0)
{
of->natoms_x_compressed++;
}
}
}
if (bCiteTng)
{
please_cite(fplog, "Lundborg2014");
}
return of;
}
int main(int argc,char *argv[])
{
const char *desc[] = {
"[TT]do_multiprot[tt] ",
"reads a trajectory file and aligns it to a reference structure ",
"each time frame",
"calling the multiprot program. This allows you to use a reference",
"structure whose sequence is different than that of the protein in the ",
"trajectory, since the alignment is based on the geometry, not sequence.",
"The output of [TT]do_multiprot[tt] includes the rmsd and the number of residues",
"on which it was calculated.",
"[PAR]",
"An aligned trajectory file is generated with the [TT]-ox[tt] option.[PAR]",
"With the [TT]-cr[tt] option, the number of hits in the alignment is given",
"per residue. This number can be between 0 and the number of frames, and",
"indicates the structural conservation of this residue.[PAR]",
"If you do not have the [TT]multiprot[tt] program, get it. [TT]do_multiprot[tt] assumes",
"that the [TT]multiprot[tt] executable is [TT]/usr/local/bin/multiprot[tt]. If this is ",
"not the case, then you should set an environment variable [BB]MULTIPROT[bb]",
"pointing to the [TT]multiprot[tt] executable, e.g.: [PAR]",
"[TT]setenv MULTIPROT /usr/MultiProtInstall/multiprot.Linux[tt][PAR]",
"Note that at the current implementation only binary alignment (your",
"molecule to a reference) is supported. In addition, note that the ",
"by default [TT]multiprot[tt] aligns the two proteins on their C-alpha carbons.",
"and that this depends on the [TT]multiprot[tt] parameters which are not dealt ",
"with here. Thus, the C-alpha carbons is expected to give the same "
"results as choosing the whole protein and will be slightly faster.[PAR]",
"For information about [TT]multiprot[tt], see:",
"http://bioinfo3d.cs.tau.ac.il/MultiProt/.[PAR]"
};
static bool bVerbose;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"HIDDENGenerate miles of useless information" }
};
const char *bugs[] = {
"The program is very slow, since multiprot is run externally"
};
t_trxstatus *status;
t_trxstatus *trxout=NULL;
FILE *tapein,*fo,*frc,*tmpf,*out=NULL,*fres=NULL;
const char *fnRef;
const char *fn="2_sol.res";
t_topology top;
int ePBC;
t_atoms *atoms,ratoms,useatoms;
t_trxframe fr;
t_pdbinfo p;
int nres,nres2,nr0;
real t;
int i,j,natoms,nratoms,nframe=0,model_nr=-1;
int cur_res,prev_res;
int nout;
t_countres *countres=NULL;
matrix box,rbox;
int gnx;
char *grpnm,*ss_str;
atom_id *index;
rvec *xp,*x,*xr;
char pdbfile[32],refpdb[256],title[256],rtitle[256],filemode[5];
char out_title[256];
char multiprot[256],*mptr;
int ftp;
int outftp=-1;
real rmsd;
bool bTrjout,bCountres;
const char *TrjoutFile=NULL;
output_env_t oenv;
static rvec translation={0,0,0},rotangles={0,0,0};
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTX, "-r", NULL , ffREAD },
{ efXVG, "-o", "rmss", ffWRITE },
{ efXVG, "-rc", "rescount", ffWRITE},
{ efXVG, "-cr", "countres", ffOPTWR},
{ efTRX, "-ox", "aligned", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE,fnm, asize(pa),pa, asize(desc),desc,
asize(bugs),bugs,&oenv
);
fnRef=opt2fn("-r",NFILE,fnm);
bTrjout = opt2bSet("-ox",NFILE,fnm);
bCountres= opt2bSet("-cr",NFILE,fnm);
if (bTrjout) {
TrjoutFile = opt2fn_null("-ox",NFILE,fnm);
}
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xp,NULL,box,FALSE);
gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,box);
atoms=&(top.atoms);
ftp=fn2ftp(fnRef);
get_stx_coordnum(fnRef,&nratoms);
init_t_atoms(&ratoms,nratoms,TRUE);
snew(xr,nratoms);
read_stx_conf(fnRef,rtitle,&ratoms,xr,NULL,&ePBC,rbox);
if (bVerbose) {
fprintf(stderr,"Read %d atoms\n",atoms->nr);
fprintf(stderr,"Read %d reference atoms\n",ratoms.nr);
}
if (bCountres) {
snew(countres,ratoms.nres);
j=0;
cur_res=0;
for (i=0;i<ratoms.nr;i++) {
prev_res=cur_res;
cur_res=ratoms.atom[i].resind;
if (cur_res != prev_res) {
countres[j].resnr=cur_res;
countres[j].count=0;
j++;
}
}
}
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
nres=0;
nr0=-1;
for(i=0; (i<gnx); i++) {
if (atoms->atom[index[i]].resind != nr0) {
nr0=atoms->atom[index[i]].resind;
nres++;
}
}
fprintf(stderr,"There are %d residues in your selected group\n",nres);
strcpy(pdbfile,"ddXXXXXX");
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
sprintf(pdbfile,"%ctmp%cfilterXXXXXX",DIR_SEPARATOR,DIR_SEPARATOR);
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
gmx_fatal(FARGS,"Can not open tmp file %s",pdbfile);
}
}
else {
gmx_ffclose(tmpf);
}
if (ftp != efPDB) {
strcpy(refpdb,"ddXXXXXX");
gmx_tmpnam(refpdb);
strcat(refpdb,".pdb");
write_sto_conf(refpdb,rtitle,&ratoms,xr,NULL,ePBC,rbox);
}
else {
strcpy(refpdb,fnRef);
}
if ((mptr=getenv("MULTIPROT")) == NULL) {
mptr="/usr/local/bin/multiprot";
}
if (!gmx_fexist(mptr)) {
gmx_fatal(FARGS,"MULTIPROT executable (%s) does not exist (use setenv MULTIPROT)",
mptr);
}
sprintf (multiprot,"%s %s %s > /dev/null %s",
mptr, refpdb, pdbfile, "2> /dev/null");
if (bVerbose)
fprintf(stderr,"multiprot cmd='%s'\n",multiprot);
if (!read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_READ_X))
gmx_fatal(FARGS,"Could not read a frame from %s",ftp2fn(efTRX,NFILE,fnm));
natoms = fr.natoms;
if (bTrjout) {
nout=natoms;
/* open file now */
outftp=fn2ftp(TrjoutFile);
if (bVerbose)
fprintf(stderr,"Will write %s: %s\n",ftp2ext(ftp),ftp2desc(outftp));
strcpy(filemode,"w");
switch (outftp) {
case efXTC:
case efG87:
case efTRR:
case efTRJ:
out=NULL;
trxout = open_trx(TrjoutFile,filemode);
break;
case efGRO:
case efG96:
case efPDB:
/* Make atoms struct for output in GRO or PDB files */
/* get memory for stuff to go in pdb file */
init_t_atoms(&useatoms,nout,FALSE);
sfree(useatoms.resinfo);
useatoms.resinfo=atoms->resinfo;
for(i=0;(i<nout);i++) {
useatoms.atomname[i]=atoms->atomname[i];
useatoms.atom[i]=atoms->atom[i];
useatoms.nres=max(useatoms.nres,useatoms.atom[i].resind+1);
}
useatoms.nr=nout;
out=gmx_ffopen(TrjoutFile,filemode);
break;
}
}
if (natoms > atoms->nr) {
gmx_fatal(FARGS,"\nTrajectory does not match topology!");
}
if (gnx > natoms) {
gmx_fatal(FARGS,"\nTrajectory does not match selected group!");
}
fo = xvgropen(opt2fn("-o",NFILE,fnm),"RMSD","Time (ps)","RMSD (nm)",oenv);
frc = xvgropen(opt2fn("-rc",NFILE,fnm),"Number of Residues in the alignment","Time (ps)","Residues",oenv);
do {
t = output_env_conv_time(oenv,fr.time);
gmx_rmpbc(gpbc,natoms,fr.box,fr.x);
tapein=gmx_ffopen(pdbfile,"w");
write_pdbfile_indexed(tapein,NULL,atoms,fr.x,ePBC,fr.box,' ',-1,gnx,index,NULL,TRUE);
gmx_ffclose(tapein);
system(multiprot);
remove(pdbfile);
process_multiprot_output(fn, &rmsd, &nres2,rotangles,translation,bCountres,countres);
fprintf(fo,"%12.7f",t);
fprintf(fo," %12.7f\n",rmsd);
fprintf(frc,"%12.7f",t);
fprintf(frc,"%12d\n",nres2);
if (bTrjout) {
rotate_conf(natoms,fr.x,NULL,rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<natoms; i++) {
rvec_inc(fr.x[i],translation);
}
switch(outftp) {
case efTRJ:
case efTRR:
case efG87:
case efXTC:
write_trxframe(trxout,&fr,NULL);
break;
case efGRO:
case efG96:
case efPDB:
sprintf(out_title,"Generated by do_multiprot : %s t= %g %s",
title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
switch(outftp) {
case efGRO:
write_hconf_p(out,out_title,&useatoms,prec2ndec(fr.prec),
fr.x,NULL,fr.box);
break;
case efPDB:
fprintf(out,"REMARK GENERATED BY DO_MULTIPROT\n");
sprintf(out_title,"%s t= %g %s",title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
/* if reading from pdb, we want to keep the original
model numbering else we write the output frame
number plus one, because model 0 is not allowed in pdb */
if (ftp==efPDB && fr.step > model_nr) {
model_nr = fr.step;
}
else {
model_nr++;
}
write_pdbfile(out,out_title,&useatoms,fr.x,ePBC,fr.box,' ',model_nr,NULL,TRUE);
break;
case efG96:
fr.title = out_title;
fr.bTitle = (nframe == 0);
fr.bAtoms = FALSE;
fr.bStep = TRUE;
fr.bTime = TRUE;
write_g96_conf(out,&fr,-1,NULL);
}
break;
}
}
nframe++;
} while(read_next_frame(oenv,status,&fr));
if (bCountres) {
fres= xvgropen(opt2fn("-cr",NFILE,fnm),"Number of frames in which the residues are aligned to","Residue","Number",oenv);
for (i=0;i<ratoms.nres;i++) {
fprintf(fres,"%10d %12d\n",countres[i].resnr,countres[i].count);
}
gmx_ffclose(fres);
}
gmx_ffclose(fo);
gmx_ffclose(frc);
fprintf(stderr,"\n");
close_trj(status);
if (trxout != NULL) {
close_trx(trxout);
}
else if (out != NULL) {
gmx_ffclose(out);
}
view_all(oenv,NFILE, fnm);
sfree(xr);
if (bCountres) {
sfree(countres);
}
free_t_atoms(&ratoms,TRUE);
if (bTrjout) {
if (outftp==efPDB || outftp==efGRO || outftp==efG96) {
free_t_atoms(&useatoms,TRUE);
}
}
gmx_thanx(stderr);
return 0;
}
int gmx_sdf(int argc,char *argv[])
{
const char *desc[] = {
"g_sdf calculates the spatial distribution function (SDF) of a set of atoms",
"within a coordinate system defined by three atoms. There is single body, ",
"two body and three body SDF implemented (select with option -mode). ",
"In the single body case the local coordinate system is defined by using",
"a triple of atoms from one single molecule, for the two and three body case",
"the configurations are dynamically searched complexes of two or three",
"molecules (or residues) meeting certain distance consitions (see below).[PAR]",
"The program needs a trajectory, a GROMACS run input file and an index ",
"file to work. ",
"You have to setup 4 groups in the index file before using g_sdf: [PAR]",
"The first three groups are used to define the SDF coordinate system.",
"The programm will dynamically generate the atom tripels according to ",
"the selected -mode: ",
"In -mode 1 the triples will be just the 1st, 2nd, 3rd, ... atoms from ",
"groups 1, 2 and 3. Hence the nth entries in groups 1, 2 and 3 must be from the",
"same residue. In -mode 2 the triples will be 1st, 2nd, 3rd, ... atoms from",
"groups 1 and 2 (with the nth entries in groups 1 and 2 having the same res-id).",
"For each pair from groups 1 and 2 group 3 is searched for an atom meeting the",
"distance conditions set with -triangle and -dtri relative to atoms 1 and 2. In",
"-mode 3 for each atom in group 1 group 2 is searched for an atom meeting the",
"distance condition and if a pair is found group 3 is searched for an atom",
"meeting the further conditions. The triple will only be used if all three atoms",
"have different res-id's.[PAR]",
"The local coordinate system is always defined using the following scheme:",
"Atom 1 will be used as the point of origin for the SDF. "
"Atom 1 and 2 will define the principle axis (Z) of the coordinate system.",
"The other two axis will be defined inplane (Y) and normal (X) to the plane through",
"Atoms 1, 2 and 3. "
"The fourth group",
"contains the atoms for which the SDF will be evaluated.[PAR]",
"For -mode 2 and 3 you have to define the distance conditions for the ",
"2 resp. 3 molecule complexes to be searched for using -triangle and -dtri.[PAR]",
"The SDF will be sampled in cartesian coordinates.",
"Use '-grid x y z' to define the size of the SDF grid around the ",
"reference molecule. ",
"The Volume of the SDF grid will be V=x*y*z (nm^3). "
"Use -bin to set the binwidth for grid.[PAR]",
"The output will be a binary 3D-grid file (gom_plt.dat) in the .plt format that can be be",
"read directly by gOpenMol. ",
"The option -r will generate a .gro file with the reference molecule(s) transfered to",
"the SDF coordinate system. Load this file into gOpenMol and display the",
"SDF as a contour plot (see http://www.csc.fi/gopenmol/index.phtml for ",
"further documentation). [PAR]",
"For further information about SDF's have a look at: A. Vishnyakov, JPC A, 105,",
"2001, 1702 and the references cited within."
};
static bool bRef=FALSE;
static int mode=1;
static rvec triangle={0.0,0.0,0.0};
static rvec dtri={0.03,0.03,0.03};
static rvec cutoff={1,1,1};
static real binwidth=0.05;
t_pargs pa[] = {
{ "-mode", FALSE, etINT, {&mode},
"SDF in [1,2,3] particle mode"},
{ "-triangle", FALSE, etRVEC, {&triangle},
"r(1,3), r(2,3), r(1,2)"},
{ "-dtri", FALSE, etRVEC, {&dtri},
"dr(1,3), dr(2,3), dr(1,2)"},
{ "-bin", FALSE, etREAL, {&binwidth},
"Binwidth for the 3D-grid (nm)" },
{ "-grid", FALSE, etRVEC, {&cutoff},
"Size of the 3D-grid (nm,nm,nm)"}
};
#define NPA asize(pa)
char *fnTPS,*fnNDX,*fnREF;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffOPTRD },
{ efDAT, "-o", "gom_plt", ffWRITE },
{ efSTO, "-r", "refmol", ffOPTWR },
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
fnTPS = ftp2fn_null(efTPS,NFILE,fnm);
fnNDX = ftp2fn_null(efNDX,NFILE,fnm);
fnREF = opt2fn_null("-r",NFILE,fnm);
bRef = opt2bSet("-r",NFILE,fnm);
if (!fnNDX)
gmx_fatal(FARGS,"No index file specified\n"
" Nothing to do!");
if (!fnTPS)
gmx_fatal(FARGS,"No topology file specified\n"
" Nothing to do!");
if ( bRef && fn2ftp(fnREF) != efGRO)
{
fprintf(stderr,"\nOnly GROMACS format is supported for reference structures.\n");
fprintf(stderr,"Option -r will be ignored!\n");
bRef = FALSE;
}
if (mode < 1 || mode > 3)
gmx_fatal(FARGS,"Wrong -mode selection. Chose 1-, 2- oder 3-praticle mode.\n");
do_sdf(fnNDX,fnTPS,ftp2fn(efTRX,NFILE,fnm),opt2fn("-o",NFILE,fnm),
fnREF,bRef,cutoff,binwidth,mode,triangle,dtri);
thanx(stderr);
return 0;
}
int gmx_dyecoupl(int argc, char *argv[])
{
const char *desc[] =
{
"[THISMODULE] extracts dye dynamics from trajectory files.",
"Currently, R and kappa^2 between dyes is extracted for (F)RET",
"simulations with assumed dipolar coupling as in the Foerster equation.",
"It further allows the calculation of R(t) and kappa^2(t), R and",
"kappa^2 histograms and averages, as well as the instantaneous FRET",
"efficiency E(t) for a specified Foerster radius R_0 (switch [TT]-R0[tt]).",
"The input dyes have to be whole (see res and mol pbc options",
"in [TT]trjconv[tt]).",
"The dye transition dipole moment has to be defined by at least",
"a single atom pair, however multiple atom pairs can be provided ",
"in the index file. The distance R is calculated on the basis of",
"the COMs of the given atom pairs.",
"The [TT]-pbcdist[tt] option calculates distances to the nearest periodic",
"image instead to the distance in the box. This works however only,"
"for periodic boundaries in all 3 dimensions.",
"The [TT]-norm[tt] option (area-) normalizes the histograms."
};
static gmx_bool bPBCdist = FALSE, bNormHist = FALSE;
int histbins = 50;
gmx_output_env_t *oenv;
real R0 = -1;
t_pargs pa[] =
{
{ "-pbcdist", FALSE, etBOOL, { &bPBCdist }, "Distance R based on PBC" },
{ "-norm", FALSE, etBOOL, { &bNormHist }, "Normalize histograms" },
{ "-bins", FALSE, etINT, {&histbins}, "# of histogram bins" },
{ "-R0", FALSE, etREAL, {&R0}, "Foerster radius including kappa^2=2/3 in nm" }
};
#define NPA asize(pa)
t_filenm fnm[] =
{
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efXVG, "-ot", "rkappa", ffOPTWR },
{ efXVG, "-oe", "insteff", ffOPTWR },
{ efDAT, "-o", "rkappa", ffOPTWR },
{ efXVG, "-rhist", "rhist", ffOPTWR },
{ efXVG, "-khist", "khist", ffOPTWR }
};
#define NFILE asize(fnm)
const char *in_trajfile, *out_xvgrkfile = NULL, *out_xvginstefffile = NULL, *out_xvgrhistfile = NULL, *out_xvgkhistfile = NULL, *out_datfile = NULL;
gmx_bool bHaveFirstFrame, bHaveNextFrame, indexOK = TRUE;
int ndon, nacc;
atom_id *donindex, *accindex;
char *grpnm;
t_trxstatus *status;
t_trxframe fr;
int flags;
int allocblock = 1000;
real histexpand = 1e-6;
rvec donvec, accvec, donpos, accpos, dist, distnorm;
int natoms;
/*we rely on PBC autodetection (...currently)*/
int ePBC = -1;
real *rvalues = NULL, *kappa2values = NULL, *rhist = NULL, *khist = NULL;
t_pbc *pbc = NULL;
int i, bin;
FILE *rkfp = NULL, *rhfp = NULL, *khfp = NULL, *datfp = NULL, *iefp = NULL;
gmx_bool bRKout, bRhistout, bKhistout, bDatout, bInstEffout, grident;
const char *rkleg[2] = { "R", "\\f{Symbol}k\\f{}\\S2\\N" };
const char *rhleg[1] = { "p(R)" };
const char *khleg[1] = { "p(\\f{Symbol}k\\f{}\\S2\\N)" };
const char *ieleg[1] = { "E\\sRET\\N(t)" };
real R, kappa2, insteff, Rs = 0., kappa2s = 0., insteffs = 0., rmax, rmin, kmin = 0., kmax = 4.,
rrange, krange, rincr, kincr, Rfrac;
int rkcount = 0, rblocksallocated = 0, kblocksallocated = 0;
if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* Check command line options for filenames and set bool flags when switch used*/
in_trajfile = opt2fn("-f", NFILE, fnm);
out_xvgrkfile = opt2fn("-ot", NFILE, fnm);
out_xvgrhistfile = opt2fn("-rhist", NFILE, fnm);
out_xvgkhistfile = opt2fn("-khist", NFILE, fnm);
out_xvginstefffile = opt2fn("-oe", NFILE, fnm);
out_datfile = opt2fn("-o", NFILE, fnm);
bRKout = opt2bSet("-ot", NFILE, fnm);
bRhistout = opt2bSet("-rhist", NFILE, fnm);
bKhistout = opt2bSet("-khist", NFILE, fnm);
bDatout = opt2bSet("-o", NFILE, fnm);
bInstEffout = opt2bSet("-oe", NFILE, fnm);
/* PBC warning. */
if (bPBCdist)
{
printf("Calculating distances to periodic image.\n");
printf("Be careful! This produces only valid results for PBC in all three dimensions\n");
}
if (bInstEffout && R0 <= 0.)
{
gmx_fatal(FARGS, "You have to specify R0 and R0 has to be larger than 0 nm.\n\n");
}
printf("Select group with donor atom pairs defining the transition moment\n");
get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
printf("Select group with acceptor atom pairs defining the transition moment\n");
get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
/*check if groups are identical*/
grident = TRUE;
if (ndon == nacc)
{
for (i = 0; i < nacc; i++)
{
if (accindex[i] != donindex[i])
{
grident = FALSE;
break;
}
}
}
if (grident)
{
gmx_fatal(FARGS, "Donor and acceptor group are identical. This makes no sense.");
}
printf("Reading first frame\n");
/* open trx file for reading */
flags = 0;
flags = flags | TRX_READ_X;
bHaveFirstFrame = read_first_frame(oenv, &status, in_trajfile, &fr, flags);
if (bHaveFirstFrame)
{
printf("First frame is OK\n");
natoms = fr.natoms;
if ((ndon % 2 != 0) || (nacc % 2 != 0))
{
indexOK = FALSE;
}
else
{
for (i = 0; i < ndon; i++)
{
if (donindex[i] >= natoms)
{
indexOK = FALSE;
}
}
for (i = 0; i < nacc; i++)
{
if (accindex[i] >= natoms)
{
indexOK = FALSE;
}
}
}
if (indexOK)
{
if (bDatout)
{
datfp = gmx_ffopen(out_datfile, "w");
}
if (bRKout)
{
rkfp = xvgropen(out_xvgrkfile,
"Distance and \\f{Symbol}k\\f{}\\S2\\N trajectory",
"Time (ps)", "Distance (nm) / \\f{Symbol}k\\f{}\\S2\\N",
oenv);
xvgr_legend(rkfp, 2, rkleg, oenv);
}
if (bInstEffout)
{
iefp = xvgropen(out_xvginstefffile,
"Instantaneous RET Efficiency",
"Time (ps)", "RET Efficiency",
oenv);
xvgr_legend(iefp, 1, ieleg, oenv);
}
if (bRhistout)
{
snew(rvalues, allocblock);
rblocksallocated += 1;
snew(rhist, histbins);
}
if (bKhistout)
{
snew(kappa2values, allocblock);
kblocksallocated += 1;
snew(khist, histbins);
}
do
{
clear_rvec(donvec);
clear_rvec(accvec);
clear_rvec(donpos);
clear_rvec(accpos);
for (i = 0; i < ndon / 2; i++)
{
rvec_sub(donvec, fr.x[donindex[2 * i]], donvec);
rvec_add(donvec, fr.x[donindex[2 * i + 1]], donvec);
rvec_add(donpos, fr.x[donindex[2 * i]], donpos);
rvec_add(donpos, fr.x[donindex[2 * i + 1]], donpos);
}
for (i = 0; i < nacc / 2; i++)
{
rvec_sub(accvec, fr.x[accindex[2 * i]], accvec);
rvec_add(accvec, fr.x[accindex[2 * i + 1]], accvec);
rvec_add(accpos, fr.x[accindex[2 * i]], accpos);
rvec_add(accpos, fr.x[accindex[2 * i + 1]], accpos);
}
unitv(donvec, donvec);
unitv(accvec, accvec);
svmul(1.0 / ndon, donpos, donpos);
svmul(1.0 / nacc, accpos, accpos);
if (bPBCdist)
{
set_pbc(pbc, ePBC, fr.box);
pbc_dx(pbc, donpos, accpos, dist);
}
else
{
rvec_sub(donpos, accpos, dist);
}
unitv(dist, distnorm);
R = norm(dist);
kappa2 = iprod(donvec, accvec)- 3.* (iprod(donvec, distnorm) * iprod(distnorm, accvec));
kappa2 *= kappa2;
if (R0 > 0)
{
Rfrac = R/R0;
insteff = 1/(1+(Rfrac*Rfrac*Rfrac*Rfrac*Rfrac*Rfrac)*2/3/kappa2);
insteffs += insteff;
if (bInstEffout)
{
fprintf(iefp, "%12.7f %12.7f\n", fr.time, insteff);
}
}
Rs += R;
kappa2s += kappa2;
rkcount++;
if (bRKout)
{
fprintf(rkfp, "%12.7f %12.7f %12.7f\n", fr.time, R, kappa2);
}
if (bDatout)
{
fprintf(datfp, "%12.7f %12.7f %12.7f\n", fr.time, R, kappa2);
}
if (bRhistout)
{
rvalues[rkcount-1] = R;
if (rkcount % allocblock == 0)
{
srenew(rvalues, allocblock*(rblocksallocated+1));
rblocksallocated += 1;
}
}
if (bKhistout)
{
kappa2values[rkcount-1] = kappa2;
if (rkcount % allocblock == 0)
{
srenew(kappa2values, allocblock*(kblocksallocated+1));
kblocksallocated += 1;
}
}
bHaveNextFrame = read_next_frame(oenv, status, &fr);
}
while (bHaveNextFrame);
if (bRKout)
{
xvgrclose(rkfp);
}
if (bDatout)
{
gmx_ffclose(datfp);
}
if (bInstEffout)
{
xvgrclose(iefp);
}
if (bRhistout)
{
printf("Writing R-Histogram\n");
rmin = rvalues[0];
rmax = rvalues[0];
for (i = 1; i < rkcount; i++)
{
if (rvalues[i] < rmin)
{
rmin = rvalues[i];
}
else if (rvalues[i] > rmax)
{
rmax = rvalues[i];
}
}
rmin -= histexpand;
rmax += histexpand;
rrange = rmax - rmin;
rincr = rrange / histbins;
for (i = 1; i < rkcount; i++)
{
bin = static_cast<int>((rvalues[i] - rmin) / rincr);
rhist[bin] += 1;
}
if (bNormHist)
{
for (i = 0; i < histbins; i++)
{
rhist[i] /= rkcount * rrange/histbins;
}
rhfp = xvgropen(out_xvgrhistfile, "Distance Distribution",
"R (nm)", "Normalized Probability", oenv);
}
else
{
rhfp = xvgropen(out_xvgrhistfile, "Distance Distribution",
"R (nm)", "Probability", oenv);
}
xvgr_legend(rhfp, 1, rhleg, oenv);
for (i = 0; i < histbins; i++)
{
fprintf(rhfp, "%12.7f %12.7f\n", (i + 0.5) * rincr + rmin,
rhist[i]);
}
xvgrclose(rhfp);
}
if (bKhistout)
{
printf("Writing kappa^2-Histogram\n");
krange = kmax - kmin;
kincr = krange / histbins;
for (i = 1; i < rkcount; i++)
{
bin = static_cast<int>((kappa2values[i] - kmin) / kincr);
khist[bin] += 1;
}
if (bNormHist)
{
for (i = 0; i < histbins; i++)
{
khist[i] /= rkcount * krange/histbins;
}
khfp = xvgropen(out_xvgkhistfile,
"\\f{Symbol}k\\f{}\\S2\\N Distribution",
"\\f{Symbol}k\\f{}\\S2\\N",
"Normalized Probability", oenv);
}
else
{
khfp = xvgropen(out_xvgkhistfile,
"\\f{Symbol}k\\f{}\\S2\\N Distribution",
"\\f{Symbol}k\\f{}\\S2\\N", "Probability", oenv);
}
xvgr_legend(khfp, 1, khleg, oenv);
for (i = 0; i < histbins; i++)
{
fprintf(khfp, "%12.7f %12.7f\n", (i + 0.5) * kincr + kmin,
khist[i]);
}
xvgrclose(khfp);
}
printf("\nAverages:\n");
printf("R_avg = %8.4f nm\nKappa^2 = %8.4f\n", Rs / rkcount,
kappa2s / rkcount);
if (R0 > 0)
{
printf("E_RETavg = %8.4f\n", insteffs / rkcount);
}
please_cite(stdout, "Hoefling2011");
}
else
{
gmx_fatal(FARGS, "Index file invalid, check your index file for correct pairs.\n");
}
}
else
{
gmx_fatal(FARGS, "Could not read first frame of the trajectory.\n");
}
return 0;
}
int gmx_g_angle(int argc, char *argv[])
{
static const char *desc[] = {
"[TT]g_angle[tt] computes the angle distribution for a number of angles",
"or dihedrals.[PAR]",
"With option [TT]-ov[tt], you can plot the average angle of",
"a group of angles as a function of time. With the [TT]-all[tt] option,",
"the first graph is the average and the rest are the individual angles.[PAR]",
"With the [TT]-of[tt] option, [TT]g_angle[tt] also calculates the fraction of trans",
"dihedrals (only for dihedrals) as function of time, but this is",
"probably only fun for a select few.[PAR]",
"With option [TT]-oc[tt], a dihedral correlation function is calculated.[PAR]",
"It should be noted that the index file must contain",
"atom triplets for angles or atom quadruplets for dihedrals.",
"If this is not the case, the program will crash.[PAR]",
"With option [TT]-or[tt], a trajectory file is dumped containing cos and",
"sin of selected dihedral angles, which subsequently can be used as",
"input for a principal components analysis using [TT]g_covar[tt].[PAR]",
"Option [TT]-ot[tt] plots when transitions occur between",
"dihedral rotamers of multiplicity 3 and [TT]-oh[tt]",
"records a histogram of the times between such transitions,",
"assuming the input trajectory frames are equally spaced in time."
};
static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
static gmx_bool bALL = FALSE, bChandler = FALSE, bAverCorr = FALSE, bPBC = TRUE;
static real binwidth = 1;
t_pargs pa[] = {
{ "-type", FALSE, etENUM, {opt},
"Type of angle to analyse"
},
{ "-all", FALSE, etBOOL, {&bALL},
"Plot all angles separately in the averages file, in the order of appearance in the index file."
},
{ "-binwidth", FALSE, etREAL, {&binwidth},
"binwidth (degrees) for calculating the distribution"
},
{ "-periodic", FALSE, etBOOL, {&bPBC},
"Print dihedral angles modulo 360 degrees"
},
{ "-chandler", FALSE, etBOOL, {&bChandler},
"Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 or phi > 60."
},
{ "-avercorr", FALSE, etBOOL, {&bAverCorr},
"Average the correlation functions for the individual angles/dihedrals"
}
};
static const char *bugs[] = {
"Counting transitions only works for dihedrals with multiplicity 3"
};
FILE *out;
real tmp, dt;
int status, isize;
atom_id *index;
char *grpname;
real maxang, Jc, S2, norm_fac, maxstat;
unsigned long mode;
int nframes, maxangstat, mult, *angstat;
int i, j, total, nangles, natoms, nat2, first, last, angind;
gmx_bool bAver, bRb, bPeriodic,
bFrac, /* calculate fraction too? */
bTrans, /* worry about transtions too? */
bCorr; /* correlation function ? */
real t, aa, aver, aver2, aversig, fraction; /* fraction trans dihedrals */
double tfrac = 0;
char title[256];
real **dih = NULL; /* mega array with all dih. angles at all times*/
char buf[80];
real *time, *trans_frac, *aver_angle;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, "angle", ffREAD },
{ efXVG, "-od", "angdist", ffWRITE },
{ efXVG, "-ov", "angaver", ffOPTWR },
{ efXVG, "-of", "dihfrac", ffOPTWR },
{ efXVG, "-ot", "dihtrans", ffOPTWR },
{ efXVG, "-oh", "trhisto", ffOPTWR },
{ efXVG, "-oc", "dihcorr", ffOPTWR },
{ efTRR, "-or", NULL, ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
output_env_t oenv;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
&oenv);
mult = 4;
maxang = 360.0;
bRb = FALSE;
switch (opt[0][0])
{
case 'a':
mult = 3;
maxang = 180.0;
break;
case 'd':
break;
case 'i':
break;
case 'r':
bRb = TRUE;
break;
}
if (opt2bSet("-or", NFILE, fnm))
{
if (mult != 4)
{
gmx_fatal(FARGS, "Can not combine angles with trn dump");
}
else
{
please_cite(stdout, "Mu2005a");
}
}
/* Calculate bin size */
maxangstat = (int)(maxang/binwidth+0.5);
binwidth = maxang/maxangstat;
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
nangles = isize/mult;
if ((isize % mult) != 0)
{
gmx_fatal(FARGS, "number of index elements not multiple of %d, "
"these can not be %s\n",
mult, (mult == 3) ? "angle triplets" : "dihedral quadruplets");
}
/* Check whether specific analysis has to be performed */
bCorr = opt2bSet("-oc", NFILE, fnm);
bAver = opt2bSet("-ov", NFILE, fnm);
bTrans = opt2bSet("-ot", NFILE, fnm);
bFrac = opt2bSet("-of", NFILE, fnm);
if (bTrans && opt[0][0] != 'd')
{
fprintf(stderr, "Option -ot should only accompany -type dihedral. Disabling -ot.\n");
bTrans = FALSE;
}
if (bChandler && !bCorr)
{
bCorr = TRUE;
}
if (bFrac && !bRb)
{
fprintf(stderr, "Warning:"
" calculating fractions as defined in this program\n"
"makes sense for Ryckaert Bellemans dihs. only. Ignoring -of\n\n");
bFrac = FALSE;
}
if ( (bTrans || bFrac || bCorr) && mult == 3)
{
gmx_fatal(FARGS, "Can only do transition, fraction or correlation\n"
"on dihedrals. Select -d\n");
}
/*
* We need to know the nr of frames so we can allocate memory for an array
* with all dihedral angles at all timesteps. Works for me.
*/
if (bTrans || bCorr || bALL || opt2bSet("-or", NFILE, fnm))
{
snew(dih, nangles);
}
snew(angstat, maxangstat);
read_ang_dih(ftp2fn(efTRX, NFILE, fnm), (mult == 3),
bALL || bCorr || bTrans || opt2bSet("-or", NFILE, fnm),
bRb, bPBC, maxangstat, angstat,
&nframes, &time, isize, index, &trans_frac, &aver_angle, dih,
oenv);
dt = (time[nframes-1]-time[0])/(nframes-1);
if (bAver)
{
sprintf(title, "Average Angle: %s", grpname);
out = xvgropen(opt2fn("-ov", NFILE, fnm),
title, "Time (ps)", "Angle (degrees)", oenv);
for (i = 0; (i < nframes); i++)
{
fprintf(out, "%10.5f %8.3f", time[i], aver_angle[i]*RAD2DEG);
if (bALL)
{
for (j = 0; (j < nangles); j++)
{
if (bPBC)
{
real dd = dih[j][i];
fprintf(out, " %8.3f", atan2(sin(dd), cos(dd))*RAD2DEG);
}
else
{
fprintf(out, " %8.3f", dih[j][i]*RAD2DEG);
}
}
}
fprintf(out, "\n");
}
ffclose(out);
}
if (opt2bSet("-or", NFILE, fnm))
{
dump_dih_trn(nframes, nangles, dih, opt2fn("-or", NFILE, fnm), time);
}
if (bFrac)
{
sprintf(title, "Trans fraction: %s", grpname);
out = xvgropen(opt2fn("-of", NFILE, fnm),
title, "Time (ps)", "Fraction", oenv);
tfrac = 0.0;
for (i = 0; (i < nframes); i++)
{
fprintf(out, "%10.5f %10.3f\n", time[i], trans_frac[i]);
tfrac += trans_frac[i];
}
ffclose(out);
tfrac /= nframes;
fprintf(stderr, "Average trans fraction: %g\n", tfrac);
}
sfree(trans_frac);
if (bTrans)
{
ana_dih_trans(opt2fn("-ot", NFILE, fnm), opt2fn("-oh", NFILE, fnm),
dih, nframes, nangles, grpname, time, bRb, oenv);
}
if (bCorr)
{
/* Autocorrelation function */
if (nframes < 2)
{
fprintf(stderr, "Not enough frames for correlation function\n");
}
else
{
if (bChandler)
{
real dval, sixty = DEG2RAD*60;
gmx_bool bTest;
for (i = 0; (i < nangles); i++)
{
for (j = 0; (j < nframes); j++)
{
dval = dih[i][j];
if (bRb)
{
bTest = (dval > -sixty) && (dval < sixty);
}
else
{
bTest = (dval < -sixty) || (dval > sixty);
}
if (bTest)
{
dih[i][j] = dval-tfrac;
}
else
{
dih[i][j] = -tfrac;
}
}
}
}
if (bChandler)
{
mode = eacNormal;
}
else
{
mode = eacCos;
}
do_autocorr(opt2fn("-oc", NFILE, fnm), oenv,
"Dihedral Autocorrelation Function",
nframes, nangles, dih, dt, mode, bAverCorr);
}
}
/* Determine the non-zero part of the distribution */
for (first = 0; (first < maxangstat-1) && (angstat[first+1] == 0); first++)
{
;
}
for (last = maxangstat-1; (last > 0) && (angstat[last-1] == 0); last--)
{
;
}
aver = aver2 = 0;
for (i = 0; (i < nframes); i++)
{
aver += RAD2DEG*aver_angle[i];
aver2 += sqr(RAD2DEG*aver_angle[i]);
}
aver /= (real) nframes;
aver2 /= (real) nframes;
aversig = sqrt(aver2-sqr(aver));
printf("Found points in the range from %d to %d (max %d)\n",
first, last, maxangstat);
printf(" < angle > = %g\n", aver);
printf("< angle^2 > = %g\n", aver2);
printf("Std. Dev. = %g\n", aversig);
if (mult == 3)
{
sprintf(title, "Angle Distribution: %s", grpname);
}
else
{
sprintf(title, "Dihedral Distribution: %s", grpname);
calc_distribution_props(maxangstat, angstat, -180.0, 0, NULL, &S2);
fprintf(stderr, "Order parameter S^2 = %g\n", S2);
}
bPeriodic = (mult == 4) && (first == 0) && (last == maxangstat-1);
out = xvgropen(opt2fn("-od", NFILE, fnm), title, "Degrees", "", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "@ subtitle \"average angle: %g\\So\\N\"\n", aver);
}
norm_fac = 1.0/(nangles*nframes*binwidth);
if (bPeriodic)
{
maxstat = 0;
for (i = first; (i <= last); i++)
{
maxstat = max(maxstat, angstat[i]*norm_fac);
}
fprintf(out, "@with g0\n");
fprintf(out, "@ world xmin -180\n");
fprintf(out, "@ world xmax 180\n");
fprintf(out, "@ world ymin 0\n");
fprintf(out, "@ world ymax %g\n", maxstat*1.05);
fprintf(out, "@ xaxis tick major 60\n");
fprintf(out, "@ xaxis tick minor 30\n");
fprintf(out, "@ yaxis tick major 0.005\n");
fprintf(out, "@ yaxis tick minor 0.0025\n");
}
for (i = first; (i <= last); i++)
{
fprintf(out, "%10g %10f\n", i*binwidth+180.0-maxang, angstat[i]*norm_fac);
}
if (bPeriodic)
{
/* print first bin again as last one */
fprintf(out, "%10g %10f\n", 180.0, angstat[0]*norm_fac);
}
ffclose(out);
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
if (bAver)
{
do_view(oenv, opt2fn("-ov", NFILE, fnm), "-nxy");
}
thanx(stderr);
return 0;
}
int cmain (int argc, char *argv[])
{
const char *desc[] = {
"tpbconv can edit run input files in four ways.[PAR]",
"[BB]1.[bb] by modifying the number of steps in a run input file",
"with options [TT]-extend[tt], [TT]-until[tt] or [TT]-nsteps[tt]",
"(nsteps=-1 means unlimited number of steps)[PAR]",
"[BB]2.[bb] (OBSOLETE) by creating a run input file",
"for a continuation run when your simulation has crashed due to e.g.",
"a full disk, or by making a continuation run input file.",
"This option is obsolete, since mdrun now writes and reads",
"checkpoint files.",
"[BB]Note[bb] that a frame with coordinates and velocities is needed.",
"When pressure and/or Nose-Hoover temperature coupling is used",
"an energy file can be supplied to get an exact continuation",
"of the original run.[PAR]",
"[BB]3.[bb] by creating a [TT].tpx[tt] file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
"your [TT].tpx[tt] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [TT].tpx[tt] file.",
"Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
"this to work.",
"[BB]WARNING: this [TT].tpx[tt] file is not fully functional[bb].[PAR]",
"[BB]4.[bb] by setting the charges of a specified group",
"to zero. This is useful when doing free energy estimates",
"using the LIE (Linear Interaction Energy) method."
};
const char *top_fn, *frame_fn;
t_fileio *fp;
ener_file_t fp_ener = NULL;
t_trnheader head;
int i;
gmx_large_int_t nsteps_req, run_step, frame;
double run_t, state_t;
gmx_bool bOK, bNsteps, bExtend, bUntil, bTime, bTraj;
gmx_bool bFrame, bUse, bSel, bNeedEner, bReadEner, bScanEner, bFepState;
gmx_mtop_t mtop;
t_atoms atoms;
t_inputrec *ir, *irnew = NULL;
t_gromppopts *gopts;
t_state state;
rvec *newx = NULL, *newv = NULL, *tmpx, *tmpv;
matrix newbox;
int gnx;
char *grpname;
atom_id *index = NULL;
int nre;
gmx_enxnm_t *enm = NULL;
t_enxframe *fr_ener = NULL;
char buf[200], buf2[200];
output_env_t oenv;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-f", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efTPX, "-o", "tpxout", ffWRITE }
};
#define NFILE asize(fnm)
/* Command line options */
static int nsteps_req_int = 0;
static real start_t = -1.0, extend_t = 0.0, until_t = 0.0;
static int init_fep_state = 0;
static gmx_bool bContinuation = TRUE, bZeroQ = FALSE, bVel = TRUE;
static t_pargs pa[] = {
{ "-extend", FALSE, etREAL, {&extend_t},
"Extend runtime by this amount (ps)" },
{ "-until", FALSE, etREAL, {&until_t},
"Extend runtime until this ending time (ps)" },
{ "-nsteps", FALSE, etINT, {&nsteps_req_int},
"Change the number of steps" },
{ "-time", FALSE, etREAL, {&start_t},
"Continue from frame at this time (ps) instead of the last frame" },
{ "-zeroq", FALSE, etBOOL, {&bZeroQ},
"Set the charges of a group (from the index) to zero" },
{ "-vel", FALSE, etBOOL, {&bVel},
"Require velocities from trajectory" },
{ "-cont", FALSE, etBOOL, {&bContinuation},
"For exact continuation, the constraints should not be applied before the first step" },
{ "-init_fep_state", FALSE, etINT, {&init_fep_state},
"fep state to initialize from" },
};
int nerror = 0;
CopyRight(stderr, argv[0]);
/* Parse the command line */
parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv);
/* Convert int to gmx_large_int_t */
nsteps_req = nsteps_req_int;
bNsteps = opt2parg_bSet("-nsteps", asize(pa), pa);
bExtend = opt2parg_bSet("-extend", asize(pa), pa);
bUntil = opt2parg_bSet("-until", asize(pa), pa);
bFepState = opt2parg_bSet("-init_fep_state", asize(pa), pa);
bTime = opt2parg_bSet("-time", asize(pa), pa);
bTraj = (opt2bSet("-f", NFILE, fnm) || bTime);
top_fn = ftp2fn(efTPX, NFILE, fnm);
fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);
snew(ir, 1);
read_tpx_state(top_fn, ir, &state, NULL, &mtop);
run_step = ir->init_step;
run_t = ir->init_step*ir->delta_t + ir->init_t;
if (!EI_STATE_VELOCITY(ir->eI))
{
bVel = FALSE;
}
if (bTraj)
{
fprintf(stderr, "\n"
"NOTE: Reading the state from trajectory is an obsolete feature of tpbconv.\n"
" Continuation should be done by loading a checkpoint file with mdrun -cpi\n"
" This guarantees that all state variables are transferred.\n"
" tpbconv is now only useful for increasing nsteps,\n"
" but even that can often be avoided by using mdrun -maxh\n"
"\n");
if (ir->bContinuation != bContinuation)
{
fprintf(stderr, "Modifying ir->bContinuation to %s\n",
bool_names[bContinuation]);
}
ir->bContinuation = bContinuation;
bNeedEner = (ir->epc == epcPARRINELLORAHMAN || ir->etc == etcNOSEHOOVER);
bReadEner = (bNeedEner && ftp2bSet(efEDR, NFILE, fnm));
bScanEner = (bReadEner && !bTime);
if (ir->epc != epcNO || EI_SD(ir->eI) || ir->eI == eiBD)
{
fprintf(stderr, "NOTE: The simulation uses pressure coupling and/or stochastic dynamics.\n"
"tpbconv can not provide binary identical continuation.\n"
"If you want that, supply a checkpoint file to mdrun\n\n");
}
if (EI_SD(ir->eI) || ir->eI == eiBD)
{
fprintf(stderr, "\nChanging ld-seed from %d ", ir->ld_seed);
ir->ld_seed = make_seed();
fprintf(stderr, "to %d\n\n", ir->ld_seed);
}
frame_fn = ftp2fn(efTRN, NFILE, fnm);
if (fn2ftp(frame_fn) == efCPT)
{
int sim_part;
fprintf(stderr,
"\nREADING STATE FROM CHECKPOINT %s...\n\n",
frame_fn);
read_checkpoint_state(frame_fn, &sim_part,
&run_step, &run_t, &state);
}
else
{
fprintf(stderr,
"\nREADING COORDS, VELS AND BOX FROM TRAJECTORY %s...\n\n",
frame_fn);
fp = open_trn(frame_fn, "r");
if (bScanEner)
{
fp_ener = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
do_enxnms(fp_ener, &nre, &enm);
snew(fr_ener, 1);
fr_ener->t = -1e-12;
}
/* Now scan until the last set of x and v (step == 0)
* or the ones at step step.
*/
bFrame = TRUE;
frame = 0;
while (bFrame)
{
bFrame = fread_trnheader(fp, &head, &bOK);
if (bOK && frame == 0)
{
if (mtop.natoms != head.natoms)
{
gmx_fatal(FARGS, "Number of atoms in Topology (%d) "
"is not the same as in Trajectory (%d)\n",
mtop.natoms, head.natoms);
}
snew(newx, head.natoms);
snew(newv, head.natoms);
}
bFrame = bFrame && bOK;
if (bFrame)
{
bOK = fread_htrn(fp, &head, newbox, newx, newv, NULL);
}
bFrame = bFrame && bOK;
bUse = FALSE;
if (bFrame &&
(head.x_size) && (head.v_size || !bVel))
{
bUse = TRUE;
if (bScanEner)
{
/* Read until the energy time is >= the trajectory time */
while (fr_ener->t < head.t && do_enx(fp_ener, fr_ener))
{
;
}
bUse = (fr_ener->t == head.t);
}
if (bUse)
{
tmpx = newx;
newx = state.x;
state.x = tmpx;
tmpv = newv;
newv = state.v;
state.v = tmpv;
run_t = head.t;
run_step = head.step;
state.fep_state = head.fep_state;
state.lambda[efptFEP] = head.lambda;
copy_mat(newbox, state.box);
}
}
if (bFrame || !bOK)
{
sprintf(buf, "\r%s %s frame %s%s: step %s%s time %s",
"%s", "%s", "%6", gmx_large_int_fmt, "%6", gmx_large_int_fmt, " %8.3f");
fprintf(stderr, buf,
bUse ? "Read " : "Skipped", ftp2ext(fn2ftp(frame_fn)),
frame, head.step, head.t);
frame++;
if (bTime && (head.t >= start_t))
{
bFrame = FALSE;
}
}
}
if (bScanEner)
{
close_enx(fp_ener);
free_enxframe(fr_ener);
free_enxnms(nre, enm);
}
close_trn(fp);
fprintf(stderr, "\n");
if (!bOK)
{
fprintf(stderr, "%s frame %s (step %s, time %g) is incomplete\n",
ftp2ext(fn2ftp(frame_fn)), gmx_step_str(frame-1, buf2),
gmx_step_str(head.step, buf), head.t);
}
fprintf(stderr, "\nUsing frame of step %s time %g\n",
gmx_step_str(run_step, buf), run_t);
if (bNeedEner)
{
if (bReadEner)
{
get_enx_state(ftp2fn(efEDR, NFILE, fnm), run_t, &mtop.groups, ir, &state);
}
else
{
fprintf(stderr, "\nWARNING: The simulation uses %s temperature and/or %s pressure coupling,\n"
" the continuation will only be exact when an energy file is supplied\n\n",
ETCOUPLTYPE(etcNOSEHOOVER),
EPCOUPLTYPE(epcPARRINELLORAHMAN));
}
}
if (bFepState)
{
ir->fepvals->init_fep_state = init_fep_state;
}
}
}
if (bNsteps)
{
fprintf(stderr, "Setting nsteps to %s\n", gmx_step_str(nsteps_req, buf));
ir->nsteps = nsteps_req;
}
else
{
/* Determine total number of steps remaining */
if (bExtend)
{
ir->nsteps = ir->nsteps - (run_step - ir->init_step) + (gmx_large_int_t)(extend_t/ir->delta_t + 0.5);
printf("Extending remaining runtime of by %g ps (now %s steps)\n",
extend_t, gmx_step_str(ir->nsteps, buf));
}
else if (bUntil)
{
printf("nsteps = %s, run_step = %s, current_t = %g, until = %g\n",
gmx_step_str(ir->nsteps, buf),
gmx_step_str(run_step, buf2),
run_t, until_t);
ir->nsteps = (gmx_large_int_t)((until_t - run_t)/ir->delta_t + 0.5);
printf("Extending remaining runtime until %g ps (now %s steps)\n",
until_t, gmx_step_str(ir->nsteps, buf));
}
else
{
ir->nsteps -= run_step - ir->init_step;
/* Print message */
printf("%s steps (%g ps) remaining from first run.\n",
gmx_step_str(ir->nsteps, buf), ir->nsteps*ir->delta_t);
}
}
if (bNsteps || bZeroQ || (ir->nsteps > 0))
{
ir->init_step = run_step;
if (ftp2bSet(efNDX, NFILE, fnm) ||
!(bNsteps || bExtend || bUntil || bTraj))
{
atoms = gmx_mtop_global_atoms(&mtop);
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1,
&gnx, &index, &grpname);
if (!bZeroQ)
{
bSel = (gnx != state.natoms);
for (i = 0; ((i < gnx) && (!bSel)); i++)
{
bSel = (i != index[i]);
}
}
else
{
bSel = FALSE;
}
if (bSel)
{
fprintf(stderr, "Will write subset %s of original tpx containing %d "
"atoms\n", grpname, gnx);
reduce_topology_x(gnx, index, &mtop, state.x, state.v);
state.natoms = gnx;
}
else if (bZeroQ)
{
zeroq(gnx, index, &mtop);
fprintf(stderr, "Zero-ing charges for group %s\n", grpname);
}
else
{
fprintf(stderr, "Will write full tpx file (no selection)\n");
}
}
state_t = ir->init_t + ir->init_step*ir->delta_t;
sprintf(buf, "Writing statusfile with starting step %s%s and length %s%s steps...\n", "%10", gmx_large_int_fmt, "%10", gmx_large_int_fmt);
fprintf(stderr, buf, ir->init_step, ir->nsteps);
fprintf(stderr, " time %10.3f and length %10.3f ps\n",
state_t, ir->nsteps*ir->delta_t);
write_tpx_state(opt2fn("-o", NFILE, fnm), ir, &state, &mtop);
}
else
{
printf("You've simulated long enough. Not writing tpr file\n");
}
thanx(stderr);
return 0;
}
int gmx_rms(int argc, char *argv[])
{
const char *desc[] =
{
"[THISMODULE] compares two structures by computing the root mean square",
"deviation (RMSD), the size-independent [GRK]rho[grk] similarity parameter",
"([TT]rho[tt]) or the scaled [GRK]rho[grk] ([TT]rhosc[tt]), ",
"see Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).",
"This is selected by [TT]-what[tt].[PAR]"
"Each structure from a trajectory ([TT]-f[tt]) is compared to a",
"reference structure. The reference structure",
"is taken from the structure file ([TT]-s[tt]).[PAR]",
"With option [TT]-mir[tt] also a comparison with the mirror image of",
"the reference structure is calculated.",
"This is useful as a reference for 'significant' values, see",
"Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).[PAR]",
"Option [TT]-prev[tt] produces the comparison with a previous frame",
"the specified number of frames ago.[PAR]",
"Option [TT]-m[tt] produces a matrix in [TT].xpm[tt] format of",
"comparison values of each structure in the trajectory with respect to",
"each other structure. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [gmx-xpm2ps].[PAR]",
"Option [TT]-fit[tt] controls the least-squares fitting of",
"the structures on top of each other: complete fit (rotation and",
"translation), translation only, or no fitting at all.[PAR]",
"Option [TT]-mw[tt] controls whether mass weighting is done or not.",
"If you select the option (default) and ",
"supply a valid [TT].tpr[tt] file masses will be taken from there, ",
"otherwise the masses will be deduced from the [TT]atommass.dat[tt] file in",
"[TT]GMXLIB[tt]. This is fine for proteins, but not",
"necessarily for other molecules. A default mass of 12.011 amu (carbon)",
"is assigned to unknown atoms. You can check whether this happend by",
"turning on the [TT]-debug[tt] flag and inspecting the log file.[PAR]",
"With [TT]-f2[tt], the 'other structures' are taken from a second",
"trajectory, this generates a comparison matrix of one trajectory",
"versus the other.[PAR]",
"Option [TT]-bin[tt] does a binary dump of the comparison matrix.[PAR]",
"Option [TT]-bm[tt] produces a matrix of average bond angle deviations",
"analogously to the [TT]-m[tt] option. Only bonds between atoms in the",
"comparison group are considered."
};
static gmx_bool bPBC = TRUE, bFitAll = TRUE, bSplit = FALSE;
static gmx_bool bDeltaLog = FALSE;
static int prev = 0, freq = 1, freq2 = 1, nlevels = 80, avl = 0;
static real rmsd_user_max = -1, rmsd_user_min = -1, bond_user_max = -1,
bond_user_min = -1, delta_maxy = 0.0;
/* strings and things for selecting difference method */
enum
{
ewSel, ewRMSD, ewRho, ewRhoSc, ewNR
};
int ewhat;
const char *what[ewNR + 1] =
{ NULL, "rmsd", "rho", "rhosc", NULL };
const char *whatname[ewNR] =
{ NULL, "RMSD", "Rho", "Rho sc" };
const char *whatlabel[ewNR] =
{ NULL, "RMSD (nm)", "Rho", "Rho sc" };
const char *whatxvgname[ewNR] =
{ NULL, "RMSD", "\\8r\\4", "\\8r\\4\\ssc\\N" };
const char *whatxvglabel[ewNR] =
{ NULL, "RMSD (nm)", "\\8r\\4", "\\8r\\4\\ssc\\N" };
/* strings and things for fitting methods */
enum
{
efSel, efFit, efReset, efNone, efNR
};
int efit;
const char *fit[efNR + 1] =
{ NULL, "rot+trans", "translation", "none", NULL };
const char *fitgraphlabel[efNR + 1] =
{ NULL, "lsq fit", "translational fit", "no fit" };
static int nrms = 1;
static gmx_bool bMassWeighted = TRUE;
t_pargs pa[] =
{
{ "-what", FALSE, etENUM,
{ what }, "Structural difference measure" },
{ "-pbc", FALSE, etBOOL,
{ &bPBC }, "PBC check" },
{ "-fit", FALSE, etENUM,
{ fit }, "Fit to reference structure" },
{ "-prev", FALSE, etINT,
{ &prev }, "Compare with previous frame" },
{ "-split", FALSE, etBOOL,
{ &bSplit }, "Split graph where time is zero" },
{ "-fitall", FALSE, etBOOL,
{ &bFitAll }, "HIDDENFit all pairs of structures in matrix" },
{ "-skip", FALSE, etINT,
{ &freq }, "Only write every nr-th frame to matrix" },
{ "-skip2", FALSE, etINT,
{ &freq2 }, "Only write every nr-th frame to matrix" },
{ "-max", FALSE, etREAL,
{ &rmsd_user_max }, "Maximum level in comparison matrix" },
{ "-min", FALSE, etREAL,
{ &rmsd_user_min }, "Minimum level in comparison matrix" },
{ "-bmax", FALSE, etREAL,
{ &bond_user_max }, "Maximum level in bond angle matrix" },
{ "-bmin", FALSE, etREAL,
{ &bond_user_min }, "Minimum level in bond angle matrix" },
{ "-mw", FALSE, etBOOL,
{ &bMassWeighted }, "Use mass weighting for superposition" },
{ "-nlevels", FALSE, etINT,
{ &nlevels }, "Number of levels in the matrices" },
{ "-ng", FALSE, etINT,
{ &nrms }, "Number of groups to compute RMS between" },
{ "-dlog", FALSE, etBOOL,
{ &bDeltaLog },
"HIDDENUse a log x-axis in the delta t matrix" },
{ "-dmax", FALSE, etREAL,
{ &delta_maxy }, "HIDDENMaximum level in delta matrix" },
{ "-aver", FALSE, etINT,
{ &avl },
"HIDDENAverage over this distance in the RMSD matrix" }
};
int natoms_trx, natoms_trx2, natoms;
int i, j, k, m, teller, teller2, tel_mat, tel_mat2;
#define NFRAME 5000
int maxframe = NFRAME, maxframe2 = NFRAME;
real t, *w_rls, *w_rms, *w_rls_m = NULL, *w_rms_m = NULL;
gmx_bool bNorm, bAv, bFreq2, bFile2, bMat, bBond, bDelta, bMirror, bMass;
gmx_bool bFit, bReset;
t_topology top;
int ePBC;
t_iatom *iatom = NULL;
matrix box;
rvec *x, *xp, *xm = NULL, **mat_x = NULL, **mat_x2, *mat_x2_j = NULL, vec1,
vec2;
t_trxstatus *status;
char buf[256], buf2[256];
int ncons = 0;
FILE *fp;
real rlstot = 0, **rls, **rlsm = NULL, *time, *time2, *rlsnorm = NULL,
**rmsd_mat = NULL, **bond_mat = NULL, *axis, *axis2, *del_xaxis,
*del_yaxis, rmsd_max, rmsd_min, rmsd_avg, bond_max, bond_min, ang;
real **rmsdav_mat = NULL, av_tot, weight, weight_tot;
real **delta = NULL, delta_max, delta_scalex = 0, delta_scaley = 0,
*delta_tot;
int delta_xsize = 0, del_lev = 100, mx, my, abs_my;
gmx_bool bA1, bA2, bPrev, bTop, *bInMat = NULL;
int ifit, *irms, ibond = 0, *ind_bond1 = NULL, *ind_bond2 = NULL, n_ind_m =
0;
atom_id *ind_fit, **ind_rms, *ind_m = NULL, *rev_ind_m = NULL, *ind_rms_m =
NULL;
char *gn_fit, **gn_rms;
t_rgb rlo, rhi;
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
t_filenm fnm[] =
{
{ efTPS, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efTRX, "-f2", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "rmsd", ffWRITE },
{ efXVG, "-mir", "rmsdmir", ffOPTWR },
{ efXVG, "-a", "avgrp", ffOPTWR },
{ efXVG, "-dist", "rmsd-dist", ffOPTWR },
{ efXPM, "-m", "rmsd", ffOPTWR },
{ efDAT, "-bin", "rmsd", ffOPTWR },
{ efXPM, "-bm", "bond", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW
| PCA_BE_NICE, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
&oenv))
{
return 0;
}
/* parse enumerated options: */
ewhat = nenum(what);
if (ewhat == ewRho || ewhat == ewRhoSc)
{
please_cite(stdout, "Maiorov95");
}
efit = nenum(fit);
bFit = efit == efFit;
bReset = efit == efReset;
if (bFit)
{
bReset = TRUE; /* for fit, reset *must* be set */
}
else
{
bFitAll = FALSE;
}
/* mark active cmdline options */
bMirror = opt2bSet("-mir", NFILE, fnm); /* calc RMSD vs mirror of ref. */
bFile2 = opt2bSet("-f2", NFILE, fnm);
bMat = opt2bSet("-m", NFILE, fnm);
bBond = opt2bSet("-bm", NFILE, fnm);
bDelta = (delta_maxy > 0); /* calculate rmsd vs delta t matrix from *
* your RMSD matrix (hidden option */
bNorm = opt2bSet("-a", NFILE, fnm);
bFreq2 = opt2parg_bSet("-skip2", asize(pa), pa);
if (freq <= 0)
{
fprintf(stderr, "The number of frames to skip is <= 0. "
"Writing out all frames.\n\n");
freq = 1;
}
if (!bFreq2)
{
freq2 = freq;
}
else if (bFile2 && freq2 <= 0)
{
fprintf(stderr,
"The number of frames to skip in second trajectory is <= 0.\n"
" Writing out all frames.\n\n");
freq2 = 1;
}
bPrev = (prev > 0);
if (bPrev)
{
prev = abs(prev);
if (freq != 1)
{
fprintf(stderr, "WARNING: option -skip also applies to -prev\n");
}
}
if (bFile2 && !bMat && !bBond)
{
fprintf(
stderr,
"WARNING: second trajectory (-f2) useless when not calculating matrix (-m/-bm),\n"
" will not read from %s\n", opt2fn("-f2", NFILE,
fnm));
bFile2 = FALSE;
}
if (bDelta)
{
bMat = TRUE;
if (bFile2)
{
fprintf(stderr,
"WARNING: second trajectory (-f2) useless when making delta matrix,\n"
" will not read from %s\n", opt2fn("-f2",
NFILE, fnm));
bFile2 = FALSE;
}
}
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), buf, &top, &ePBC, &xp,
NULL, box, TRUE);
snew(w_rls, top.atoms.nr);
snew(w_rms, top.atoms.nr);
if (!bTop && bBond)
{
fprintf(stderr,
"WARNING: Need a run input file for bond angle matrix,\n"
" will not calculate bond angle matrix.\n");
bBond = FALSE;
}
if (bReset)
{
fprintf(stderr, "Select group for %s fit\n", bFit ? "least squares"
: "translational");
get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &ifit,
&ind_fit, &gn_fit);
}
else
{
ifit = 0;
}
if (bReset)
{
if (bFit && ifit < 3)
{
gmx_fatal(FARGS, "Need >= 3 points to fit!\n" );
}
bMass = FALSE;
for (i = 0; i < ifit; i++)
{
if (bMassWeighted)
{
w_rls[ind_fit[i]] = top.atoms.atom[ind_fit[i]].m;
}
else
{
w_rls[ind_fit[i]] = 1;
}
bMass = bMass || (top.atoms.atom[ind_fit[i]].m != 0);
}
if (!bMass)
{
fprintf(stderr, "All masses in the fit group are 0, using masses of 1\n");
for (i = 0; i < ifit; i++)
{
w_rls[ind_fit[i]] = 1;
}
}
}
if (bMat || bBond)
{
nrms = 1;
}
snew(gn_rms, nrms);
snew(ind_rms, nrms);
snew(irms, nrms);
fprintf(stderr, "Select group%s for %s calculation\n",
(nrms > 1) ? "s" : "", whatname[ewhat]);
get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm),
nrms, irms, ind_rms, gn_rms);
if (bNorm)
{
snew(rlsnorm, irms[0]);
}
snew(rls, nrms);
for (j = 0; j < nrms; j++)
{
snew(rls[j], maxframe);
}
if (bMirror)
{
snew(rlsm, nrms);
for (j = 0; j < nrms; j++)
{
snew(rlsm[j], maxframe);
}
}
snew(time, maxframe);
for (j = 0; j < nrms; j++)
{
bMass = FALSE;
for (i = 0; i < irms[j]; i++)
{
if (bMassWeighted)
{
w_rms[ind_rms[j][i]] = top.atoms.atom[ind_rms[j][i]].m;
}
else
{
w_rms[ind_rms[j][i]] = 1.0;
}
bMass = bMass || (top.atoms.atom[ind_rms[j][i]].m != 0);
}
if (!bMass)
{
fprintf(stderr, "All masses in group %d are 0, using masses of 1\n", j);
for (i = 0; i < irms[j]; i++)
{
w_rms[ind_rms[j][i]] = 1;
}
}
}
/* Prepare reference frame */
if (bPBC)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
gmx_rmpbc(gpbc, top.atoms.nr, box, xp);
}
if (bReset)
{
reset_x(ifit, ind_fit, top.atoms.nr, NULL, xp, w_rls);
}
if (bMirror)
{
/* generate reference structure mirror image: */
snew(xm, top.atoms.nr);
for (i = 0; i < top.atoms.nr; i++)
{
copy_rvec(xp[i], xm[i]);
xm[i][XX] = -xm[i][XX];
}
}
if (ewhat == ewRhoSc)
{
norm_princ(&top.atoms, ifit, ind_fit, top.atoms.nr, xp);
}
/* read first frame */
natoms_trx = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
if (natoms_trx != top.atoms.nr)
{
fprintf(stderr,
"\nWARNING: topology has %d atoms, whereas trajectory has %d\n",
top.atoms.nr, natoms_trx);
}
natoms = min(top.atoms.nr, natoms_trx);
if (bMat || bBond || bPrev)
{
snew(mat_x, NFRAME);
if (bPrev)
{
/* With -prev we use all atoms for simplicity */
n_ind_m = natoms;
}
else
{
/* Check which atoms we need (fit/rms) */
snew(bInMat, natoms);
for (i = 0; i < ifit; i++)
{
bInMat[ind_fit[i]] = TRUE;
}
n_ind_m = ifit;
for (i = 0; i < irms[0]; i++)
{
if (!bInMat[ind_rms[0][i]])
{
bInMat[ind_rms[0][i]] = TRUE;
n_ind_m++;
}
}
}
/* Make an index of needed atoms */
snew(ind_m, n_ind_m);
snew(rev_ind_m, natoms);
j = 0;
for (i = 0; i < natoms; i++)
{
if (bPrev || bInMat[i])
{
ind_m[j] = i;
rev_ind_m[i] = j;
j++;
}
}
snew(w_rls_m, n_ind_m);
snew(ind_rms_m, irms[0]);
snew(w_rms_m, n_ind_m);
for (i = 0; i < ifit; i++)
{
w_rls_m[rev_ind_m[ind_fit[i]]] = w_rls[ind_fit[i]];
}
for (i = 0; i < irms[0]; i++)
{
ind_rms_m[i] = rev_ind_m[ind_rms[0][i]];
w_rms_m[ind_rms_m[i]] = w_rms[ind_rms[0][i]];
}
sfree(bInMat);
}
if (bBond)
{
ncons = 0;
for (k = 0; k < F_NRE; k++)
{
if (IS_CHEMBOND(k))
{
iatom = top.idef.il[k].iatoms;
ncons += top.idef.il[k].nr/3;
}
}
fprintf(stderr, "Found %d bonds in topology\n", ncons);
snew(ind_bond1, ncons);
snew(ind_bond2, ncons);
ibond = 0;
for (k = 0; k < F_NRE; k++)
{
if (IS_CHEMBOND(k))
{
iatom = top.idef.il[k].iatoms;
ncons = top.idef.il[k].nr/3;
for (i = 0; i < ncons; i++)
{
bA1 = FALSE;
bA2 = FALSE;
for (j = 0; j < irms[0]; j++)
{
if (iatom[3*i+1] == ind_rms[0][j])
{
bA1 = TRUE;
}
if (iatom[3*i+2] == ind_rms[0][j])
{
bA2 = TRUE;
}
}
if (bA1 && bA2)
{
ind_bond1[ibond] = rev_ind_m[iatom[3*i+1]];
ind_bond2[ibond] = rev_ind_m[iatom[3*i+2]];
ibond++;
}
}
}
}
fprintf(stderr, "Using %d bonds for bond angle matrix\n", ibond);
if (ibond == 0)
{
gmx_fatal(FARGS, "0 bonds found");
}
}
/* start looping over frames: */
tel_mat = 0;
teller = 0;
do
{
if (bPBC)
{
gmx_rmpbc(gpbc, natoms, box, x);
}
if (bReset)
{
reset_x(ifit, ind_fit, natoms, NULL, x, w_rls);
}
if (ewhat == ewRhoSc)
{
norm_princ(&top.atoms, ifit, ind_fit, natoms, x);
}
if (bFit)
{
/*do the least squares fit to original structure*/
do_fit(natoms, w_rls, xp, x);
}
if (teller % freq == 0)
{
/* keep frame for matrix calculation */
if (bMat || bBond || bPrev)
{
if (tel_mat >= NFRAME)
{
srenew(mat_x, tel_mat+1);
}
snew(mat_x[tel_mat], n_ind_m);
for (i = 0; i < n_ind_m; i++)
{
copy_rvec(x[ind_m[i]], mat_x[tel_mat][i]);
}
}
tel_mat++;
}
/*calculate energy of root_least_squares*/
if (bPrev)
{
j = tel_mat-prev-1;
if (j < 0)
{
j = 0;
}
for (i = 0; i < n_ind_m; i++)
{
copy_rvec(mat_x[j][i], xp[ind_m[i]]);
}
if (bReset)
{
reset_x(ifit, ind_fit, natoms, NULL, xp, w_rls);
}
if (bFit)
{
do_fit(natoms, w_rls, x, xp);
}
}
for (j = 0; (j < nrms); j++)
{
rls[j][teller] =
calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xp);
}
if (bNorm)
{
for (j = 0; (j < irms[0]); j++)
{
rlsnorm[j] +=
calc_similar_ind(ewhat != ewRMSD, 1, &(ind_rms[0][j]), w_rms, x, xp);
}
}
if (bMirror)
{
if (bFit)
{
/*do the least squares fit to mirror of original structure*/
do_fit(natoms, w_rls, xm, x);
}
for (j = 0; j < nrms; j++)
{
rlsm[j][teller] =
calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xm);
}
}
time[teller] = output_env_conv_time(oenv, t);
teller++;
if (teller >= maxframe)
{
maxframe += NFRAME;
srenew(time, maxframe);
for (j = 0; (j < nrms); j++)
{
srenew(rls[j], maxframe);
}
if (bMirror)
{
for (j = 0; (j < nrms); j++)
{
srenew(rlsm[j], maxframe);
}
}
}
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
if (bFile2)
{
snew(time2, maxframe2);
fprintf(stderr, "\nWill read second trajectory file\n");
snew(mat_x2, NFRAME);
natoms_trx2 =
read_first_x(oenv, &status, opt2fn("-f2", NFILE, fnm), &t, &x, box);
if (natoms_trx2 != natoms_trx)
{
gmx_fatal(FARGS,
"Second trajectory (%d atoms) does not match the first one"
" (%d atoms)", natoms_trx2, natoms_trx);
}
tel_mat2 = 0;
teller2 = 0;
do
{
if (bPBC)
{
gmx_rmpbc(gpbc, natoms, box, x);
}
if (bReset)
{
reset_x(ifit, ind_fit, natoms, NULL, x, w_rls);
}
if (ewhat == ewRhoSc)
{
norm_princ(&top.atoms, ifit, ind_fit, natoms, x);
}
if (bFit)
{
/*do the least squares fit to original structure*/
do_fit(natoms, w_rls, xp, x);
}
if (teller2 % freq2 == 0)
{
/* keep frame for matrix calculation */
if (bMat)
{
if (tel_mat2 >= NFRAME)
{
srenew(mat_x2, tel_mat2+1);
}
snew(mat_x2[tel_mat2], n_ind_m);
for (i = 0; i < n_ind_m; i++)
{
copy_rvec(x[ind_m[i]], mat_x2[tel_mat2][i]);
}
}
tel_mat2++;
}
time2[teller2] = output_env_conv_time(oenv, t);
teller2++;
if (teller2 >= maxframe2)
{
maxframe2 += NFRAME;
srenew(time2, maxframe2);
}
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
}
else
{
mat_x2 = mat_x;
time2 = time;
tel_mat2 = tel_mat;
freq2 = freq;
}
gmx_rmpbc_done(gpbc);
if (bMat || bBond)
{
/* calculate RMS matrix */
fprintf(stderr, "\n");
if (bMat)
{
fprintf(stderr, "Building %s matrix, %dx%d elements\n",
whatname[ewhat], tel_mat, tel_mat2);
snew(rmsd_mat, tel_mat);
}
if (bBond)
{
fprintf(stderr, "Building bond angle matrix, %dx%d elements\n",
tel_mat, tel_mat2);
snew(bond_mat, tel_mat);
}
snew(axis, tel_mat);
snew(axis2, tel_mat2);
rmsd_max = 0;
if (bFile2)
{
rmsd_min = 1e10;
}
else
{
rmsd_min = 0;
}
rmsd_avg = 0;
bond_max = 0;
bond_min = 1e10;
for (j = 0; j < tel_mat2; j++)
{
axis2[j] = time2[freq2*j];
}
if (bDelta)
{
if (bDeltaLog)
{
delta_scalex = 8.0/log(2.0);
delta_xsize = (int)(log(tel_mat/2)*delta_scalex+0.5)+1;
}
else
{
delta_xsize = tel_mat/2;
}
delta_scaley = 1.0/delta_maxy;
snew(delta, delta_xsize);
for (j = 0; j < delta_xsize; j++)
{
snew(delta[j], del_lev+1);
}
if (avl > 0)
{
snew(rmsdav_mat, tel_mat);
for (j = 0; j < tel_mat; j++)
{
snew(rmsdav_mat[j], tel_mat);
}
}
}
if (bFitAll)
{
snew(mat_x2_j, natoms);
}
for (i = 0; i < tel_mat; i++)
{
axis[i] = time[freq*i];
fprintf(stderr, "\r element %5d; time %5.2f ", i, axis[i]);
if (bMat)
{
snew(rmsd_mat[i], tel_mat2);
}
if (bBond)
{
snew(bond_mat[i], tel_mat2);
}
for (j = 0; j < tel_mat2; j++)
{
if (bFitAll)
{
for (k = 0; k < n_ind_m; k++)
{
copy_rvec(mat_x2[j][k], mat_x2_j[k]);
}
do_fit(n_ind_m, w_rls_m, mat_x[i], mat_x2_j);
}
else
{
mat_x2_j = mat_x2[j];
}
if (bMat)
{
if (bFile2 || (i < j))
{
rmsd_mat[i][j] =
calc_similar_ind(ewhat != ewRMSD, irms[0], ind_rms_m,
w_rms_m, mat_x[i], mat_x2_j);
if (rmsd_mat[i][j] > rmsd_max)
{
rmsd_max = rmsd_mat[i][j];
}
if (rmsd_mat[i][j] < rmsd_min)
{
rmsd_min = rmsd_mat[i][j];
}
rmsd_avg += rmsd_mat[i][j];
}
else
{
rmsd_mat[i][j] = rmsd_mat[j][i];
}
}
if (bBond)
{
if (bFile2 || (i <= j))
{
ang = 0.0;
for (m = 0; m < ibond; m++)
{
rvec_sub(mat_x[i][ind_bond1[m]], mat_x[i][ind_bond2[m]], vec1);
rvec_sub(mat_x2_j[ind_bond1[m]], mat_x2_j[ind_bond2[m]], vec2);
ang += acos(cos_angle(vec1, vec2));
}
bond_mat[i][j] = ang*180.0/(M_PI*ibond);
if (bond_mat[i][j] > bond_max)
{
bond_max = bond_mat[i][j];
}
if (bond_mat[i][j] < bond_min)
{
bond_min = bond_mat[i][j];
}
}
else
{
bond_mat[i][j] = bond_mat[j][i];
}
}
}
}
if (bFile2)
{
rmsd_avg /= tel_mat*tel_mat2;
}
else
{
rmsd_avg /= tel_mat*(tel_mat - 1)/2;
}
if (bMat && (avl > 0))
{
rmsd_max = 0.0;
rmsd_min = 0.0;
rmsd_avg = 0.0;
for (j = 0; j < tel_mat-1; j++)
{
for (i = j+1; i < tel_mat; i++)
{
av_tot = 0;
weight_tot = 0;
for (my = -avl; my <= avl; my++)
{
if ((j+my >= 0) && (j+my < tel_mat))
{
abs_my = abs(my);
for (mx = -avl; mx <= avl; mx++)
{
if ((i+mx >= 0) && (i+mx < tel_mat))
{
weight = (real)(avl+1-max(abs(mx), abs_my));
av_tot += weight*rmsd_mat[i+mx][j+my];
weight_tot += weight;
}
}
}
}
rmsdav_mat[i][j] = av_tot/weight_tot;
rmsdav_mat[j][i] = rmsdav_mat[i][j];
if (rmsdav_mat[i][j] > rmsd_max)
{
rmsd_max = rmsdav_mat[i][j];
}
}
}
rmsd_mat = rmsdav_mat;
}
if (bMat)
{
fprintf(stderr, "\n%s: Min %f, Max %f, Avg %f\n",
whatname[ewhat], rmsd_min, rmsd_max, rmsd_avg);
rlo.r = 1; rlo.g = 1; rlo.b = 1;
rhi.r = 0; rhi.g = 0; rhi.b = 0;
if (rmsd_user_max != -1)
{
rmsd_max = rmsd_user_max;
}
if (rmsd_user_min != -1)
{
rmsd_min = rmsd_user_min;
}
if ((rmsd_user_max != -1) || (rmsd_user_min != -1))
{
fprintf(stderr, "Min and Max value set to resp. %f and %f\n",
rmsd_min, rmsd_max);
}
sprintf(buf, "%s %s matrix", gn_rms[0], whatname[ewhat]);
write_xpm(opt2FILE("-m", NFILE, fnm, "w"), 0, buf, whatlabel[ewhat],
output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat, tel_mat2,
axis, axis2, rmsd_mat, rmsd_min, rmsd_max, rlo, rhi, &nlevels);
/* Print the distribution of RMSD values */
if (opt2bSet("-dist", NFILE, fnm))
{
low_rmsd_dist(opt2fn("-dist", NFILE, fnm), rmsd_max, tel_mat, rmsd_mat, oenv);
}
if (bDelta)
{
snew(delta_tot, delta_xsize);
for (j = 0; j < tel_mat-1; j++)
{
for (i = j+1; i < tel_mat; i++)
{
mx = i-j;
if (mx < tel_mat/2)
{
if (bDeltaLog)
{
mx = (int)(log(mx)*delta_scalex+0.5);
}
my = (int)(rmsd_mat[i][j]*delta_scaley*del_lev+0.5);
delta_tot[mx] += 1.0;
if ((rmsd_mat[i][j] >= 0) && (rmsd_mat[i][j] <= delta_maxy))
{
delta[mx][my] += 1.0;
}
}
}
}
delta_max = 0;
for (i = 0; i < delta_xsize; i++)
{
if (delta_tot[i] > 0.0)
{
delta_tot[i] = 1.0/delta_tot[i];
for (j = 0; j <= del_lev; j++)
{
delta[i][j] *= delta_tot[i];
if (delta[i][j] > delta_max)
{
delta_max = delta[i][j];
}
}
}
}
fprintf(stderr, "Maximum in delta matrix: %f\n", delta_max);
snew(del_xaxis, delta_xsize);
snew(del_yaxis, del_lev+1);
for (i = 0; i < delta_xsize; i++)
{
del_xaxis[i] = axis[i]-axis[0];
}
for (i = 0; i < del_lev+1; i++)
{
del_yaxis[i] = delta_maxy*i/del_lev;
}
sprintf(buf, "%s %s vs. delta t", gn_rms[0], whatname[ewhat]);
fp = gmx_ffopen("delta.xpm", "w");
write_xpm(fp, 0, buf, "density", output_env_get_time_label(oenv), whatlabel[ewhat],
delta_xsize, del_lev+1, del_xaxis, del_yaxis,
delta, 0.0, delta_max, rlo, rhi, &nlevels);
gmx_ffclose(fp);
}
if (opt2bSet("-bin", NFILE, fnm))
{
/* NB: File must be binary if we use fwrite */
fp = ftp2FILE(efDAT, NFILE, fnm, "wb");
for (i = 0; i < tel_mat; i++)
{
if (fwrite(rmsd_mat[i], sizeof(**rmsd_mat), tel_mat2, fp) != tel_mat2)
{
gmx_fatal(FARGS, "Error writing to output file");
}
}
gmx_ffclose(fp);
}
}
if (bBond)
{
fprintf(stderr, "\nMin. angle: %f, Max. angle: %f\n", bond_min, bond_max);
if (bond_user_max != -1)
{
bond_max = bond_user_max;
}
if (bond_user_min != -1)
{
bond_min = bond_user_min;
}
if ((bond_user_max != -1) || (bond_user_min != -1))
{
fprintf(stderr, "Bond angle Min and Max set to:\n"
"Min. angle: %f, Max. angle: %f\n", bond_min, bond_max);
}
rlo.r = 1; rlo.g = 1; rlo.b = 1;
rhi.r = 0; rhi.g = 0; rhi.b = 0;
sprintf(buf, "%s av. bond angle deviation", gn_rms[0]);
write_xpm(opt2FILE("-bm", NFILE, fnm, "w"), 0, buf, "degrees",
output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat, tel_mat2,
axis, axis2, bond_mat, bond_min, bond_max, rlo, rhi, &nlevels);
}
}
bAv = opt2bSet("-a", NFILE, fnm);
/* Write the RMSD's to file */
if (!bPrev)
{
sprintf(buf, "%s", whatxvgname[ewhat]);
}
else
{
sprintf(buf, "%s with frame %g %s ago", whatxvgname[ewhat],
time[prev*freq]-time[0], output_env_get_time_label(oenv));
}
fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
whatxvglabel[ewhat], oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"%s%s after %s%s%s\"\n",
(nrms == 1) ? "" : "of ", gn_rms[0], fitgraphlabel[efit],
bFit ? " to " : "", bFit ? gn_fit : "");
}
if (nrms != 1)
{
xvgr_legend(fp, nrms, (const char**)gn_rms, oenv);
}
for (i = 0; (i < teller); i++)
{
if (bSplit && i > 0 &&
abs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
{
fprintf(fp, "&\n");
}
fprintf(fp, "%12.7f", time[bPrev ? freq*i : i]);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, " %12.7f", rls[j][i]);
if (bAv)
{
rlstot += rls[j][i];
}
}
fprintf(fp, "\n");
}
gmx_ffclose(fp);
if (bMirror)
{
/* Write the mirror RMSD's to file */
sprintf(buf, "%s with Mirror", whatxvgname[ewhat]);
sprintf(buf2, "Mirror %s", whatxvglabel[ewhat]);
fp = xvgropen(opt2fn("-mir", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
buf2, oenv);
if (nrms == 1)
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n",
gn_rms[0], gn_fit);
}
}
else
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"after lsq fit to mirror %s\"\n", gn_fit);
}
xvgr_legend(fp, nrms, (const char**)gn_rms, oenv);
}
for (i = 0; (i < teller); i++)
{
if (bSplit && i > 0 && abs(time[i]) < 1e-5)
{
fprintf(fp, "&\n");
}
fprintf(fp, "%12.7f", time[i]);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, " %12.7f", rlsm[j][i]);
}
fprintf(fp, "\n");
}
gmx_ffclose(fp);
}
if (bAv)
{
sprintf(buf, "Average %s", whatxvgname[ewhat]);
sprintf(buf2, "Average %s", whatxvglabel[ewhat]);
fp = xvgropen(opt2fn("-a", NFILE, fnm), buf, "Residue", buf2, oenv);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, "%10d %10g\n", j, rlstot/teller);
}
gmx_ffclose(fp);
}
if (bNorm)
{
fp = xvgropen("aver.xvg", gn_rms[0], "Residue", whatxvglabel[ewhat], oenv);
for (j = 0; (j < irms[0]); j++)
{
fprintf(fp, "%10d %10g\n", j, rlsnorm[j]/teller);
}
gmx_ffclose(fp);
}
do_view(oenv, opt2fn_null("-a", NFILE, fnm), "-graphtype bar");
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-mir", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-m", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-bm", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-dist", NFILE, fnm), NULL);
return 0;
}
int gmx_velacc(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the velocity autocorrelation function.",
"When the [TT]-m[tt] option is used, the momentum autocorrelation",
"function is calculated.[PAR]",
"With option [TT]-mol[tt] the velocity autocorrelation function of",
"molecules is calculated. In this case the index group should consist",
"of molecule numbers instead of atom numbers.[PAR]",
"Be sure that your trajectory contains frames with velocity information",
"(i.e. [TT]nstvout[tt] was set in your original [REF].mdp[ref] file),",
"and that the time interval between data collection points is",
"much shorter than the time scale of the autocorrelation."
};
static gmx_bool bMass = FALSE, bMol = FALSE, bRecip = TRUE;
t_pargs pa[] = {
{ "-m", FALSE, etBOOL, {&bMass},
"Calculate the momentum autocorrelation function" },
{ "-recip", FALSE, etBOOL, {&bRecip},
"Use cm^-1 on X-axis instead of 1/ps for spectra." },
{ "-mol", FALSE, etBOOL, {&bMol},
"Calculate the velocity acf of molecules" }
};
t_topology top;
int ePBC = -1;
t_trxframe fr;
matrix box;
gmx_bool bTPS = FALSE, bTop = FALSE;
int gnx;
int *index;
char *grpname;
/* t0, t1 are the beginning and end time respectively.
* dt is the time step, mass is temp variable for atomic mass.
*/
real t0, t1, dt, mass;
t_trxstatus *status;
int counter, n_alloc, i, j, counter_dim, k, l;
rvec mv_mol;
/* Array for the correlation function */
real **c1;
real *normm = NULL;
gmx_output_env_t *oenv;
#define NHISTO 360
t_filenm fnm[] = {
{ efTRN, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-o", "vac", ffWRITE },
{ efXVG, "-os", "spectrum", ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
sfree(ppa);
return 0;
}
if (bMol || bMass)
{
bTPS = ftp2bSet(efTPS, NFILE, fnm) || !ftp2bSet(efNDX, NFILE, fnm);
}
if (bTPS)
{
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, NULL, NULL, box,
TRUE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
}
else
{
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
}
if (bMol)
{
if (!bTop)
{
gmx_fatal(FARGS, "Need a topology to determine the molecules");
}
snew(normm, top.atoms.nr);
precalc(top, normm);
index_atom2mol(&gnx, index, &top.mols);
}
/* Correlation stuff */
snew(c1, gnx);
for (i = 0; (i < gnx); i++)
{
c1[i] = NULL;
}
read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_V);
t0 = fr.time;
n_alloc = 0;
counter = 0;
do
{
if (counter >= n_alloc)
{
n_alloc += 100;
for (i = 0; i < gnx; i++)
{
srenew(c1[i], DIM*n_alloc);
}
}
counter_dim = DIM*counter;
if (bMol)
{
for (i = 0; i < gnx; i++)
{
clear_rvec(mv_mol);
k = top.mols.index[index[i]];
l = top.mols.index[index[i]+1];
for (j = k; j < l; j++)
{
if (bMass)
{
mass = top.atoms.atom[j].m;
}
else
{
mass = normm[j];
}
mv_mol[XX] += mass*fr.v[j][XX];
mv_mol[YY] += mass*fr.v[j][YY];
mv_mol[ZZ] += mass*fr.v[j][ZZ];
}
c1[i][counter_dim+XX] = mv_mol[XX];
c1[i][counter_dim+YY] = mv_mol[YY];
c1[i][counter_dim+ZZ] = mv_mol[ZZ];
}
}
else
{
for (i = 0; i < gnx; i++)
{
if (bMass)
{
mass = top.atoms.atom[index[i]].m;
}
else
{
mass = 1;
}
c1[i][counter_dim+XX] = mass*fr.v[index[i]][XX];
c1[i][counter_dim+YY] = mass*fr.v[index[i]][YY];
c1[i][counter_dim+ZZ] = mass*fr.v[index[i]][ZZ];
}
}
t1 = fr.time;
counter++;
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
if (counter >= 4)
{
/* Compute time step between frames */
dt = (t1-t0)/(counter-1);
do_autocorr(opt2fn("-o", NFILE, fnm), oenv,
bMass ?
"Momentum Autocorrelation Function" :
"Velocity Autocorrelation Function",
counter, gnx, c1, dt, eacVector, TRUE);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
if (opt2bSet("-os", NFILE, fnm))
{
calc_spectrum(counter/2, (real *) (c1[0]), (t1-t0)/2, opt2fn("-os", NFILE, fnm),
oenv, bRecip);
do_view(oenv, opt2fn("-os", NFILE, fnm), "-nxy");
}
}
else
{
fprintf(stderr, "Not enough frames in trajectory - no output generated.\n");
}
return 0;
}
int gmx_mdrun(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"test particle insertion or (re)calculation of energies.",
"Normal mode analysis is another option. In this case [TT]mdrun[tt]",
"builds a Hessian matrix from single conformation.",
"For usual Normal Modes-like calculations, make sure that",
"the structure provided is properly energy-minimized.",
"The generated matrix can be diagonalized by [gmx-nmeig].[PAR]",
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over ranks if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each rank writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
"A simulation can be run in parallel using two different parallelization",
"schemes: MPI parallelization and/or OpenMP thread parallelization.",
"The MPI parallelization uses multiple processes when [TT]mdrun[tt] is",
"compiled with a normal MPI library or threads when [TT]mdrun[tt] is",
"compiled with the GROMACS built-in thread-MPI library. OpenMP threads",
"are supported when [TT]mdrun[tt] is compiled with OpenMP. Full OpenMP support",
"is only available with the Verlet cut-off scheme, with the (older)",
"group scheme only PME-only ranks can use OpenMP parallelization.",
"In all cases [TT]mdrun[tt] will by default try to use all the available",
"hardware resources. With a normal MPI library only the options",
"[TT]-ntomp[tt] (with the Verlet cut-off scheme) and [TT]-ntomp_pme[tt],",
"for PME-only ranks, can be used to control the number of threads.",
"With thread-MPI there are additional options [TT]-nt[tt], which sets",
"the total number of threads, and [TT]-ntmpi[tt], which sets the number",
"of thread-MPI threads.",
"The number of OpenMP threads used by [TT]mdrun[tt] can also be set with",
"the standard environment variable, [TT]OMP_NUM_THREADS[tt].",
"The [TT]GMX_PME_NUM_THREADS[tt] environment variable can be used to specify",
"the number of threads used by the PME-only ranks.[PAR]",
"Note that combined MPI+OpenMP parallelization is in many cases",
"slower than either on its own. However, at high parallelization, using the",
"combination is often beneficial as it reduces the number of domains and/or",
"the number of MPI ranks. (Less and larger domains can improve scaling,",
"with separate PME ranks, using fewer MPI ranks reduces communication costs.)",
"OpenMP-only parallelization is typically faster than MPI-only parallelization",
"on a single CPU(-die). Since we currently don't have proper hardware",
"topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
"automatically use OpenMP-only parallelization when you use up to 4",
"threads, up to 12 threads with Intel Nehalem/Westmere, or up to 16",
"threads with Intel Sandy Bridge or newer CPUs. Otherwise MPI-only",
"parallelization is used (except with GPUs, see below).",
"[PAR]",
"To quickly test the performance of the new Verlet cut-off scheme",
"with old [TT].tpr[tt] files, either on CPUs or CPUs+GPUs, you can use",
"the [TT]-testverlet[tt] option. This should not be used for production,",
"since it can slightly modify potentials and it will remove charge groups",
"making analysis difficult, as the [TT].tpr[tt] file will still contain",
"charge groups. For production simulations it is highly recommended",
"to specify [TT]cutoff-scheme = Verlet[tt] in the [TT].mdp[tt] file.",
"[PAR]",
"With GPUs (only supported with the Verlet cut-off scheme), the number",
"of GPUs should match the number of particle-particle ranks, i.e.",
"excluding PME-only ranks. With thread-MPI, unless set on the command line, the number",
"of MPI threads will automatically be set to the number of GPUs detected.",
"To use a subset of the available GPUs, or to manually provide a mapping of",
"GPUs to PP ranks, you can use the [TT]-gpu_id[tt] option. The argument of [TT]-gpu_id[tt] is",
"a string of digits (without delimiter) representing device id-s of the GPUs to be used.",
"For example, \"[TT]02[tt]\" specifies using GPUs 0 and 2 in the first and second PP ranks per compute node",
"respectively. To select different sets of GPU-s",
"on different nodes of a compute cluster, use the [TT]GMX_GPU_ID[tt] environment",
"variable instead. The format for [TT]GMX_GPU_ID[tt] is identical to ",
"[TT]-gpu_id[tt], with the difference that an environment variable can have",
"different values on different compute nodes. Multiple MPI ranks on each node",
"can share GPUs. This is accomplished by specifying the id(s) of the GPU(s)",
"multiple times, e.g. \"[TT]0011[tt]\" for four ranks sharing two GPUs in this node.",
"This works within a single simulation, or a multi-simulation, with any form of MPI.",
"[PAR]",
"With the Verlet cut-off scheme and verlet-buffer-tolerance set,",
"the pair-list update interval nstlist can be chosen freely with",
"the option [TT]-nstlist[tt]. [TT]mdrun[tt] will then adjust",
"the pair-list cut-off to maintain accuracy, and not adjust nstlist.",
"Otherwise, by default, [TT]mdrun[tt] will try to increase the",
"value of nstlist set in the [TT].mdp[tt] file to improve the",
"performance. For CPU-only runs, nstlist might increase to 20, for",
"GPU runs up to 40. For medium to high parallelization or with",
"fast GPUs, a (user-supplied) larger nstlist value can give much",
"better performance.",
"[PAR]",
"When using PME with separate PME ranks or with a GPU, the two major",
"compute tasks, the non-bonded force calculation and the PME calculation",
"run on different compute resources. If this load is not balanced,",
"some of the resources will be idle part of time. With the Verlet",
"cut-off scheme this load is automatically balanced when the PME load",
"is too high (but not when it is too low). This is done by scaling",
"the Coulomb cut-off and PME grid spacing by the same amount. In the first",
"few hundred steps different settings are tried and the fastest is chosen",
"for the rest of the simulation. This does not affect the accuracy of",
"the results, but it does affect the decomposition of the Coulomb energy",
"into particle and mesh contributions. The auto-tuning can be turned off",
"with the option [TT]-notunepme[tt].",
"[PAR]",
"[TT]mdrun[tt] pins (sets affinity of) threads to specific cores,",
"when all (logical) cores on a compute node are used by [TT]mdrun[tt],",
"even when no multi-threading is used,",
"as this usually results in significantly better performance.",
"If the queuing systems or the OpenMP library pinned threads, we honor",
"this and don't pin again, even though the layout may be sub-optimal.",
"If you want to have [TT]mdrun[tt] override an already set thread affinity",
"or pin threads when using less cores, use [TT]-pin on[tt].",
"With SMT (simultaneous multithreading), e.g. Intel Hyper-Threading,",
"there are multiple logical cores per physical core.",
"The option [TT]-pinstride[tt] sets the stride in logical cores for",
"pinning consecutive threads. Without SMT, 1 is usually the best choice.",
"With Intel Hyper-Threading 2 is best when using half or less of the",
"logical cores, 1 otherwise. The default value of 0 do exactly that:",
"it minimizes the threads per logical core, to optimize performance.",
"If you want to run multiple [TT]mdrun[tt] jobs on the same physical node,"
"you should set [TT]-pinstride[tt] to 1 when using all logical cores.",
"When running multiple [TT]mdrun[tt] (or other) simulations on the same physical",
"node, some simulations need to start pinning from a non-zero core",
"to avoid overloading cores; with [TT]-pinoffset[tt] you can specify",
"the offset in logical cores for pinning.",
"[PAR]",
"When [TT]mdrun[tt] is started with more than 1 rank,",
"parallelization with domain decomposition is used.",
"[PAR]",
"With domain decomposition, the spatial decomposition can be set",
"with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
"The user only needs to change this when the system is very inhomogeneous.",
"Dynamic load balancing is set with the option [TT]-dlb[tt],",
"which can give a significant performance improvement,",
"especially for inhomogeneous systems. The only disadvantage of",
"dynamic load balancing is that runs are no longer binary reproducible,",
"but in most cases this is not important.",
"By default the dynamic load balancing is automatically turned on",
"when the measured performance loss due to load imbalance is 5% or more.",
"At low parallelization these are the only important options",
"for domain decomposition.",
"At high parallelization the options in the next two sections",
"could be important for increasing the performace.",
"[PAR]",
"When PME is used with domain decomposition, separate ranks can",
"be assigned to do only the PME mesh calculation;",
"this is computationally more efficient starting at about 12 ranks,",
"or even fewer when OpenMP parallelization is used.",
"The number of PME ranks is set with option [TT]-npme[tt],",
"but this cannot be more than half of the ranks.",
"By default [TT]mdrun[tt] makes a guess for the number of PME",
"ranks when the number of ranks is larger than 16. With GPUs,",
"using separate PME ranks is not selected automatically,",
"since the optimal setup depends very much on the details",
"of the hardware. In all cases, you might gain performance",
"by optimizing [TT]-npme[tt]. Performance statistics on this issue",
"are written at the end of the log file.",
"For good load balancing at high parallelization, the PME grid x and y",
"dimensions should be divisible by the number of PME ranks",
"(the simulation will run correctly also when this is not the case).",
"[PAR]",
"This section lists all options that affect the domain decomposition.",
"[PAR]",
"Option [TT]-rdd[tt] can be used to set the required maximum distance",
"for inter charge-group bonded interactions.",
"Communication for two-body bonded interactions below the non-bonded",
"cut-off distance always comes for free with the non-bonded communication.",
"Atoms beyond the non-bonded cut-off are only communicated when they have",
"missing bonded interactions; this means that the extra cost is minor",
"and nearly indepedent of the value of [TT]-rdd[tt].",
"With dynamic load balancing option [TT]-rdd[tt] also sets",
"the lower limit for the domain decomposition cell sizes.",
"By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
"the initial coordinates. The chosen value will be a balance",
"between interaction range and communication cost.",
"[PAR]",
"When inter charge-group bonded interactions are beyond",
"the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
"For pair interactions and tabulated bonds",
"that do not generate exclusions, this check can be turned off",
"with the option [TT]-noddcheck[tt].",
"[PAR]",
"When constraints are present, option [TT]-rcon[tt] influences",
"the cell size limit as well.",
"Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
"should not be beyond the smallest cell size. A error message is",
"generated when this happens and the user should change the decomposition",
"or decrease the LINCS order and increase the number of LINCS iterations.",
"By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
"in a conservative fashion. For high parallelization it can be useful",
"to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
"[PAR]",
"The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
"of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
"the cells can scale down by at least this factor. This option is used",
"for the automated spatial decomposition (when not using [TT]-dd[tt])",
"as well as for determining the number of grid pulses, which in turn",
"sets the minimum allowed cell size. Under certain circumstances",
"the value of [TT]-dds[tt] might need to be adjusted to account for",
"high or low spatial inhomogeneity of the system.",
"[PAR]",
"The option [TT]-gcom[tt] can be used to only do global communication",
"every n steps.",
"This can improve performance for highly parallel simulations",
"where this global communication step becomes the bottleneck.",
"For a global thermostat and/or barostat the temperature",
"and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
"By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
"With [TT]-rerun[tt] an input trajectory can be given for which ",
"forces and energies will be (re)calculated. Neighbor searching will be",
"performed for every frame, unless [TT]nstlist[tt] is zero",
"(see the [TT].mdp[tt] file).[PAR]",
"ED (essential dynamics) sampling and/or additional flooding potentials",
"are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
"file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
"or by using options in the essdyn menu of the WHAT IF program.",
"[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
"When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type the table file name is",
"modified in a different way: before the file extension an underscore is",
"appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
"and finally the table number of the interaction type.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [TT].mdp[tt] file.[PAR]",
"With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
"simulated in parallel.",
"As many input files/directories are required as the number of systems. ",
"The [TT]-multidir[tt] option takes a list of directories (one for each ",
"system) and runs in each of them, using the input/output file names, ",
"such as specified by e.g. the [TT]-s[tt] option, relative to these ",
"directories.",
"With [TT]-multi[tt], the system number is appended to the run input ",
"and each output filename, for instance [TT]topol.tpr[tt] becomes",
"[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
"The number of ranks per system is the total number of ranks",
"divided by the number of systems.",
"One use of this option is for NMR refinement: when distance",
"or orientation restraints are present these can be ensemble averaged",
"over all the systems.[PAR]",
"With [TT]-replex[tt] replica exchange is attempted every given number",
"of steps. The number of replicas is set with the [TT]-multi[tt] or ",
"[TT]-multidir[tt] option, described above.",
"All run input files should use a different coupling temperature,",
"the order of the files is not important. The random seed is set with",
"[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
"is performed after every exchange.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability.",
"[PAR]",
"The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
"a protein into a membrane. The data file should contain the options",
"that where passed to g_membed before. The [TT]-mn[tt] and [TT]-mp[tt]",
"both apply to this as well.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
"be printed to stderr.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"unless option [TT]-cpt[tt] is set to -1.",
"The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
"make sure that a recent state of the system is always available,",
"even when the simulation is terminated while writing a checkpoint.",
"With [TT]-cpnum[tt] all checkpoint files are kept and appended",
"with the step number.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, Gromacs just assumes a normal run and",
"starts from the first step of the [TT].tpr[tt] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
"There are three scenarios with [TT]-cpi[tt]:[PAR]",
"[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
"[TT]*[tt] all files are present with names and checksums matching those stored",
"in the checkpoint file: files are appended[PAR]",
"[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
"and will be overwritten, unless its name does not match",
"the [TT]-cpo[tt] option.",
"[PAR]",
"With checkpointing the output is appended to previously written",
"output files, unless [TT]-noappend[tt] is used or none of the previous",
"output files are present (except for the checkpoint file).",
"The integrity of the files to be appended is verified using checksums",
"which are stored in the checkpoint file. This ensures that output can",
"not be mixed up or corrupted due to file appending. When only some",
"of the previous output files are present, a fatal error is generated",
"and no old output files are modified and no new output files are opened.",
"The result with appending will be the same as from a single run.",
"The contents will be binary identical, unless you use a different number",
"of ranks or dynamic load balancing or the FFT library uses optimizations",
"through timing.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
"exceeds [TT]-maxh[tt]*0.99 hours.",
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
"step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
"pressed), it will stop after the next neighbor search step ",
"(with nstlist=0 at the next step).",
"In both cases all the usual output will be written to file.",
"When running with MPI, a signal to one of the [TT]mdrun[tt] ranks",
"is sufficient, this signal should not be sent to mpirun or",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"Interactive molecular dynamics (IMD) can be activated by using at least one",
"of the three IMD switches: The [TT]-imdterm[tt] switch allows to terminate the",
"simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
"[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
"IMD remote can be turned on by [TT]-imdpull[tt].",
"The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
"file pointed to by [TT]-if[tt] contains atom indices and forces if IMD",
"pulling is used."
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
};
t_commrec *cr;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efCOMPRESSED, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tabletf", "tabletf", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRD },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efXVG, "-eo", "edsam", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles", ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque", ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efNDX, "-dn", "dipole", ffOPTWR },
{ efRND, "-multidir", NULL, ffOPTRDMULT},
{ efDAT, "-membed", "membed", ffOPTRD },
{ efTOP, "-mp", "membed", ffOPTRD },
{ efNDX, "-mn", "membed", ffOPTRD },
{ efXVG, "-if", "imdforces", ffOPTWR },
{ efXVG, "-swap", "swapions", ffOPTWR },
{ efMDP, "-at", NULL, ffOPTRD }, /* at.cfg, only for do_md */
{ efMDP, "-addtop", NULL, ffOPTRD }, /* add additional topology */
};
#define NFILE asize(fnm)
/* Command line options ! */
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bTunePME = TRUE;
gmx_bool bTestVerlet = FALSE;
gmx_bool bVerbose = FALSE;
gmx_bool bCompact = TRUE;
gmx_bool bSepPot = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
gmx_bool bIMDwait = FALSE;
gmx_bool bIMDterm = FALSE;
gmx_bool bIMDpull = FALSE;
int npme = -1;
int nstlist = 0;
int nmultisim = 0;
int nstglobalcomm = -1;
int repl_ex_nst = 0;
int repl_ex_seed = -1;
int repl_ex_nex = 0;
int nstepout = 100;
int resetstep = -1;
gmx_int64_t nsteps = -2; /* the value -2 means that the mdp option will be used */
int imdport = 8888; /* can be almost anything, 8888 is easy to remember */
rvec realddxyz = {0, 0, 0};
const char *ddno_opt[ddnoNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
const char *thread_aff_opt[threadaffNR+1] =
{ NULL, "auto", "on", "off", NULL };
const char *nbpu_opt[] =
{ NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
real cpt_period = 15.0, max_hours = -1;
gmx_bool bAppendFiles = TRUE;
gmx_bool bKeepAndNumCPT = FALSE;
gmx_bool bResetCountersHalfWay = FALSE;
output_env_t oenv = NULL;
const char *deviceOptions = "";
/* Non transparent initialization of a complex gmx_hw_opt_t struct.
* But unfortunately we are not allowed to call a function here,
* since declarations follow below.
*/
gmx_hw_opt_t hw_opt = {
0, 0, 0, 0, threadaffSEL, 0, 0,
{ NULL, FALSE, 0, NULL }
};
t_pargs pa[] = {
{ "-dd", FALSE, etRVEC, {&realddxyz},
"Domain decomposition grid, 0 is optimize" },
{ "-ddorder", FALSE, etENUM, {ddno_opt},
"DD rank order" },
{ "-npme", FALSE, etINT, {&npme},
"Number of separate ranks to be used for PME, -1 is guess" },
{ "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
"Total number of threads to start (0 is guess)" },
{ "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
"Number of thread-MPI threads to start (0 is guess)" },
{ "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
"Number of OpenMP threads per MPI rank to start (0 is guess)" },
{ "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
"Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
{ "-pin", FALSE, etENUM, {thread_aff_opt},
"Set thread affinities" },
{ "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
"The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core" },
{ "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
"Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
{ "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
"List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
"Check for all bonded interactions with DD" },
{ "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
{ "-rdd", FALSE, etREAL, {&rdd},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
{ "-rcon", FALSE, etREAL, {&rconstr},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
{ "-dlb", FALSE, etENUM, {dddlb_opt},
"Dynamic load balancing (with DD)" },
{ "-dds", FALSE, etREAL, {&dlb_scale},
"Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
"provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
{ "-ddcsx", FALSE, etSTR, {&ddcsx},
"HIDDENA string containing a vector of the relative sizes in the x "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-ddcsy", FALSE, etSTR, {&ddcsy},
"HIDDENA string containing a vector of the relative sizes in the y "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-ddcsz", FALSE, etSTR, {&ddcsz},
"HIDDENA string containing a vector of the relative sizes in the z "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-gcom", FALSE, etINT, {&nstglobalcomm},
"Global communication frequency" },
{ "-nb", FALSE, etENUM, {&nbpu_opt},
"Calculate non-bonded interactions on" },
{ "-nstlist", FALSE, etINT, {&nstlist},
"Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
{ "-tunepme", FALSE, etBOOL, {&bTunePME},
"Optimize PME load between PP/PME ranks or GPU/CPU" },
{ "-testverlet", FALSE, etBOOL, {&bTestVerlet},
"Test the Verlet non-bonded scheme" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" },
{ "-compact", FALSE, etBOOL, {&bCompact},
"Write a compact log file" },
{ "-seppot", FALSE, etBOOL, {&bSepPot},
"Write separate V and dVdl terms for each interaction type and rank to the log file(s)" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL, {&bReproducible},
"Try to avoid optimizations that affect binary reproducibility" },
{ "-cpt", FALSE, etREAL, {&cpt_period},
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-nsteps", FALSE, etINT64, {&nsteps},
"Run this number of steps, overrides .mdp file option" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT, {&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
"Attempt replica exchange periodically with this period (steps)" },
{ "-nex", FALSE, etINT, {&repl_ex_nex},
"Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-imdport", FALSE, etINT, {&imdport},
"HIDDENIMD listening port" },
{ "-imdwait", FALSE, etBOOL, {&bIMDwait},
"HIDDENPause the simulation while no IMD client is connected" },
{ "-imdterm", FALSE, etBOOL, {&bIMDterm},
"HIDDENAllow termination of the simulation from IMD client" },
{ "-imdpull", FALSE, etBOOL, {&bIMDpull},
"HIDDENAllow pulling in the simulation from IMD client" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining wall clock time for the run" },
{ "-resetstep", FALSE, etINT, {&resetstep},
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
};
unsigned long Flags, PCA_Flags;
ivec ddxyz;
int dd_node_order;
gmx_bool bAddPart;
FILE *fplog, *fpmulti;
int sim_part, sim_part_fn;
const char *part_suffix = ".part";
char suffix[STRLEN];
int rc;
char **multidir = NULL;
cr = init_commrec();
PCA_Flags = (PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET));
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
* also comment out the version of init_forcerec in md.c
* with NULL instead of opt2fn
*/
/*
if (!MASTER(cr))
{
PCA_Flags |= PCA_NOT_READ_NODE;
}
*/
if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* we set these early because they might be used in init_multisystem()
Note that there is the potential for npme>nnodes until the number of
threads is set later on, if there's thread parallelization. That shouldn't
lead to problems. */
dd_node_order = nenum(ddno_opt);
cr->npmenodes = npme;
hw_opt.thread_affinity = nenum(thread_aff_opt);
/* now check the -multi and -multidir option */
if (opt2bSet("-multidir", NFILE, fnm))
{
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
}
if (repl_ex_nst != 0 && nmultisim < 2)
{
gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
}
if (repl_ex_nex < 0)
{
gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
}
if (nmultisim > 1)
{
#ifndef GMX_THREAD_MPI
gmx_bool bParFn = (multidir == NULL);
init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
#else
gmx_fatal(FARGS, "mdrun -multi is not supported with the thread library. "
"Please compile GROMACS with MPI support");
#endif
}
bAddPart = !bAppendFiles;
/* Check if there is ANY checkpoint file available */
sim_part = 1;
sim_part_fn = sim_part;
if (opt2bSet("-cpi", NFILE, fnm))
{
if (bSepPot && bAppendFiles)
{
gmx_fatal(FARGS, "Output file appending is not supported with -seppot");
}
bAppendFiles =
read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
fnm, cr),
&sim_part_fn, NULL, cr,
bAppendFiles, NFILE, fnm,
part_suffix, &bAddPart);
if (sim_part_fn == 0 && MULTIMASTER(cr))
{
fprintf(stdout, "No previous checkpoint file present, assuming this is a new run.\n");
}
else
{
sim_part = sim_part_fn + 1;
}
if (MULTISIM(cr) && MASTER(cr))
{
if (MULTIMASTER(cr))
{
/* Log file is not yet available, so if there's a
* problem we can only write to stderr. */
fpmulti = stderr;
}
else
{
fpmulti = NULL;
}
check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
}
}
else
{
bAppendFiles = FALSE;
}
if (!bAppendFiles)
{
sim_part_fn = sim_part;
}
if (bAddPart)
{
/* Rename all output files (except checkpoint files) */
/* create new part name first (zero-filled) */
sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
add_suffix_to_output_names(fnm, NFILE, suffix);
if (MULTIMASTER(cr))
{
fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
}
}
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
Flags = Flags | (bTestVerlet ? MD_TESTVERLET : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (sim_part > 1 ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
Flags = Flags | (bIMDwait ? MD_IMDWAIT : 0);
Flags = Flags | (bIMDterm ? MD_IMDTERM : 0);
Flags = Flags | (bIMDpull ? MD_IMDPULL : 0);
Flags = Flags | ((opt2bSet("-at", NFILE, fnm)) ? MD_ADAPTIVETEMPERING : 0);
Flags = Flags | ((opt2bSet("-addtop", NFILE, fnm)) ? MD_MULTOP : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
if ((MASTER(cr) || bSepPot) && !bAppendFiles)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
!bSepPot, Flags & MD_APPENDFILES, &fplog);
please_cite(fplog, "Hess2008b");
please_cite(fplog, "Spoel2005a");
please_cite(fplog, "Lindahl2001a");
please_cite(fplog, "Berendsen95a");
}
else if (!MASTER(cr) && bSepPot)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr, !bSepPot, Flags, &fplog);
}
else
{
fplog = NULL;
}
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
nbpu_opt[0], nstlist,
nsteps, nstepout, resetstep,
nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
pforce, cpt_period, max_hours, deviceOptions, imdport, Flags);
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bAppendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
int main(int argc,char *argv[])
{
const char *desc[] = {
#ifdef GMX_OPENMM
"This is an experimental release of GROMACS for accelerated",
"Molecular Dynamics simulations on GPU processors. Support is provided",
"by the OpenMM library (https://simtk.org/home/openmm).[PAR]",
"*Warning*[BR]",
"This release is targeted at developers and advanced users and",
"care should be taken before production use. The following should be",
"noted before using the program:[PAR]",
" * The current release runs only on modern nVidia GPU hardware with CUDA support.",
"Make sure that the necessary CUDA drivers and libraries for your operating system",
"are already installed. The CUDA SDK also should be installed in order to compile",
"the program from source (http://www.nvidia.com/object/cuda_home.html).[PAR]",
" * Multiple GPU cards are not supported.[PAR]",
" * Only a small subset of the GROMACS features and options are supported on the GPUs.",
"See below for a detailed list.[PAR]",
" * Consumer level GPU cards are known to often have problems with faulty memory.",
"It is recommended that a full memory check of the cards is done at least once",
"(for example, using the memtest=full option).",
"A partial memory check (for example, memtest=15) before and",
"after the simulation run would help spot",
"problems resulting from processor overheating.[PAR]",
" * The maximum size of the simulated systems depends on the available",
"GPU memory,for example, a GTX280 with 1GB memory has been tested with systems",
"of up to about 100,000 atoms.[PAR]",
" * In order to take a full advantage of the GPU platform features, many algorithms",
"have been implemented in a very different way than they are on the CPUs.",
"Therefore numercal correspondence between properties of the state of",
"simulated systems should not be expected. Moreover, the values will likely vary",
"when simulations are done on different GPU hardware.[PAR]",
" * Frequent retrieval of system state information such as",
"trajectory coordinates and energies can greatly influence the performance",
"of the program due to slow CPU<->GPU memory transfer speed.[PAR]",
" * MD algorithms are complex, and although the Gromacs code is highly tuned for them,",
"they often do not translate very well onto the streaming architetures.",
"Realistic expectations about the achievable speed-up from test with GTX280:",
"For small protein systems in implicit solvent using all-vs-all kernels the acceleration",
"can be as high as 20 times, but in most other setups involving cutoffs and PME the",
"acceleration is usually only ~4 times relative to a 3GHz CPU.[PAR]",
"Supported features:[PAR]",
" * Integrators: md/md-vv/md-vv-avek, sd/sd1 and bd.\n",
" * Long-range interactions (option coulombtype): Reaction-Field, Ewald, PME, and cut-off (for Implicit Solvent only)\n",
" * Temperature control: Supported only with the md/md-vv/md-vv-avek, sd/sd1 and bd integrators.\n",
" * Pressure control: Supported.\n",
" * Implicit solvent: Supported.\n",
"A detailed description can be found on the GROMACS website:\n",
"http://www.gromacs.org/gpu[PAR]",
/* From the original mdrun documentaion */
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over nodes if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each node writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
/* openmm specific information */
"Usage with OpenMM:[BR]",
"[TT]mdrun -device \"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no\"[tt][PAR]",
"Options:[PAR]",
" [TT]platform[tt] = Cuda\t\t:\tThe only available value. OpenCL support will be available in future.\n",
" [TT]memtest[tt] = 15\t\t:\tRun a partial, random GPU memory test for the given amount of seconds. A full test",
"(recommended!) can be run with \"memtest=full\". Memory testing can be disabled with \"memtest=off\".\n",
" [TT]deviceid[tt] = 0\t\t:\tSpecify the target device when multiple cards are present.",
"Only one card can be used at any given time though.\n",
" [TT]force-device[tt] = no\t\t:\tIf set to \"yes\" [TT]mdrun[tt] will be forced to execute on",
"hardware that is not officially supported. GPU acceleration can also be achieved on older",
"but Cuda capable cards, although the simulation might be too slow, and the memory limits too strict.",
#else
"The [TT]mdrun[tt] program is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"test particle insertion or (re)calculation of energies.",
"Normal mode analysis is another option. In this case [TT]mdrun[tt]",
"builds a Hessian matrix from single conformation.",
"For usual Normal Modes-like calculations, make sure that",
"the structure provided is properly energy-minimized.",
"The generated matrix can be diagonalized by [TT]g_nmeig[tt].[PAR]",
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over nodes if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each node writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
"When [TT]mdrun[tt] is started using MPI with more than 1 node, parallelization",
"is used. By default domain decomposition is used, unless the [TT]-pd[tt]",
"option is set, which selects particle decomposition.[PAR]",
"With domain decomposition, the spatial decomposition can be set",
"with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
"The user only needs to change this when the system is very inhomogeneous.",
"Dynamic load balancing is set with the option [TT]-dlb[tt],",
"which can give a significant performance improvement,",
"especially for inhomogeneous systems. The only disadvantage of",
"dynamic load balancing is that runs are no longer binary reproducible,",
"but in most cases this is not important.",
"By default the dynamic load balancing is automatically turned on",
"when the measured performance loss due to load imbalance is 5% or more.",
"At low parallelization these are the only important options",
"for domain decomposition.",
"At high parallelization the options in the next two sections",
"could be important for increasing the performace.",
"[PAR]",
"When PME is used with domain decomposition, separate nodes can",
"be assigned to do only the PME mesh calculation;",
"this is computationally more efficient starting at about 12 nodes.",
"The number of PME nodes is set with option [TT]-npme[tt],",
"this can not be more than half of the nodes.",
"By default [TT]mdrun[tt] makes a guess for the number of PME",
"nodes when the number of nodes is larger than 11 or performance wise",
"not compatible with the PME grid x dimension.",
"But the user should optimize npme. Performance statistics on this issue",
"are written at the end of the log file.",
"For good load balancing at high parallelization, the PME grid x and y",
"dimensions should be divisible by the number of PME nodes",
"(the simulation will run correctly also when this is not the case).",
"[PAR]",
"This section lists all options that affect the domain decomposition.",
"[PAR]",
"Option [TT]-rdd[tt] can be used to set the required maximum distance",
"for inter charge-group bonded interactions.",
"Communication for two-body bonded interactions below the non-bonded",
"cut-off distance always comes for free with the non-bonded communication.",
"Atoms beyond the non-bonded cut-off are only communicated when they have",
"missing bonded interactions; this means that the extra cost is minor",
"and nearly indepedent of the value of [TT]-rdd[tt].",
"With dynamic load balancing option [TT]-rdd[tt] also sets",
"the lower limit for the domain decomposition cell sizes.",
"By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
"the initial coordinates. The chosen value will be a balance",
"between interaction range and communication cost.",
"[PAR]",
"When inter charge-group bonded interactions are beyond",
"the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
"For pair interactions and tabulated bonds",
"that do not generate exclusions, this check can be turned off",
"with the option [TT]-noddcheck[tt].",
"[PAR]",
"When constraints are present, option [TT]-rcon[tt] influences",
"the cell size limit as well.",
"Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
"should not be beyond the smallest cell size. A error message is",
"generated when this happens and the user should change the decomposition",
"or decrease the LINCS order and increase the number of LINCS iterations.",
"By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
"in a conservative fashion. For high parallelization it can be useful",
"to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
"[PAR]",
"The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
"of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
"the cells can scale down by at least this factor. This option is used",
"for the automated spatial decomposition (when not using [TT]-dd[tt])",
"as well as for determining the number of grid pulses, which in turn",
"sets the minimum allowed cell size. Under certain circumstances",
"the value of [TT]-dds[tt] might need to be adjusted to account for",
"high or low spatial inhomogeneity of the system.",
"[PAR]",
"The option [TT]-gcom[tt] can be used to only do global communication",
"every n steps.",
"This can improve performance for highly parallel simulations",
"where this global communication step becomes the bottleneck.",
"For a global thermostat and/or barostat the temperature",
"and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
"By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
"With [TT]-rerun[tt] an input trajectory can be given for which ",
"forces and energies will be (re)calculated. Neighbor searching will be",
"performed for every frame, unless [TT]nstlist[tt] is zero",
"(see the [TT].mdp[tt] file).[PAR]",
"ED (essential dynamics) sampling is switched on by using the [TT]-ei[tt]",
"flag followed by an [TT].edi[tt] file.",
"The [TT].edi[tt] file can be produced using options in the essdyn",
"menu of the WHAT IF program. [TT]mdrun[tt] produces a [TT].edo[tt] file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
"When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type the table file name is",
"modified in a different way: before the file extension an underscore is",
"appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
"and finally the table number of the interaction type.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [TT].mdp[tt] file.[PAR]",
"With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
"simulated in parallel.",
"As many input files/directories are required as the number of systems. ",
"The [TT]-multidir[tt] option takes a list of directories (one for each ",
"system) and runs in each of them, using the input/output file names, ",
"such as specified by e.g. the [TT]-s[tt] option, relative to these ",
"directories.",
"With [TT]-multi[tt], the system number is appended to the run input ",
"and each output filename, for instance [TT]topol.tpr[tt] becomes",
"[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
"The number of nodes per system is the total number of nodes",
"divided by the number of systems.",
"One use of this option is for NMR refinement: when distance",
"or orientation restraints are present these can be ensemble averaged",
"over all the systems.[PAR]",
"With [TT]-replex[tt] replica exchange is attempted every given number",
"of steps. The number of replicas is set with the [TT]-multi[tt] or ",
"[TT]-multidir[tt] option, described above.",
"All run input files should use a different coupling temperature,",
"the order of the files is not important. The random seed is set with",
"[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
"is performed after every exchange.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability and X-ray bombardments.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
"be printed to stderr.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"unless option [TT]-cpt[tt] is set to -1.",
"The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
"make sure that a recent state of the system is always available,",
"even when the simulation is terminated while writing a checkpoint.",
"With [TT]-cpnum[tt] all checkpoint files are kept and appended",
"with the step number.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, Gromacs just assumes a normal run and",
"starts from the first step of the [TT].tpr[tt] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
"There are three scenarios with [TT]-cpi[tt]:[PAR]",
"[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
"[TT]*[tt] all files are present with names and checksums matching those stored",
"in the checkpoint file: files are appended[PAR]",
"[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
"and will be overwritten, unless its name does not match",
"the [TT]-cpo[tt] option.",
"[PAR]",
"With checkpointing the output is appended to previously written",
"output files, unless [TT]-noappend[tt] is used or none of the previous",
"output files are present (except for the checkpoint file).",
"The integrity of the files to be appended is verified using checksums",
"which are stored in the checkpoint file. This ensures that output can",
"not be mixed up or corrupted due to file appending. When only some",
"of the previous output files are present, a fatal error is generated",
"and no old output files are modified and no new output files are opened.",
"The result with appending will be the same as from a single run.",
"The contents will be binary identical, unless you use a different number",
"of nodes or dynamic load balancing or the FFT library uses optimizations",
"through timing.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
"exceeds [TT]-maxh[tt]*0.99 hours.",
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
"step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
"pressed), it will stop after the next neighbor search step ",
"(with nstlist=0 at the next step).",
"In both cases all the usual output will be written to file.",
"When running with MPI, a signal to one of the [TT]mdrun[tt] processes",
"is sufficient, this signal should not be sent to mpirun or",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
#endif
};
t_commrec *cr;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efXTC, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tabletf", "tabletf", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRD },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efEDO, "-eo", "sam", ffOPTWR },
{ efGCT, "-j", "wham", ffOPTRD },
{ efGCT, "-jo", "bam", ffOPTWR },
{ efXVG, "-ffout", "gct", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles",ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque",ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efNDX, "-dn", "dipole", ffOPTWR },
{ efRND, "-multidir",NULL, ffOPTRDMULT},
{ efGMX, "-mmcg", "mmcg", ffOPTRD },
{ efWPO, "-wpot", "wpot", ffOPTRD }
};
#define NFILE asize(fnm)
/* Command line options ! */
gmx_bool bCart = FALSE;
gmx_bool bPPPME = FALSE;
gmx_bool bPartDec = FALSE;
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bVerbose = FALSE;
gmx_bool bCompact = TRUE;
gmx_bool bSepPot = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bIonize = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
int npme=-1;
int nmultisim=0;
int nstglobalcomm=-1;
int repl_ex_nst=0;
int repl_ex_seed=-1;
int nstepout=100;
int nthreads=0; /* set to determine # of threads automatically */
int resetstep=-1;
rvec realddxyz={0,0,0};
const char *ddno_opt[ddnoNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
char *ddcsx=NULL,*ddcsy=NULL,*ddcsz=NULL;
real cpt_period=15.0,max_hours=-1;
gmx_bool bAppendFiles=TRUE;
gmx_bool bKeepAndNumCPT=FALSE;
gmx_bool bResetCountersHalfWay=FALSE;
output_env_t oenv=NULL;
const char *deviceOptions = "";
t_pargs pa[] = {
{ "-pd", FALSE, etBOOL,{&bPartDec},
"Use particle decompostion" },
{ "-dd", FALSE, etRVEC,{&realddxyz},
"Domain decomposition grid, 0 is optimize" },
#ifdef GMX_THREADS
{ "-nt", FALSE, etINT, {&nthreads},
"Number of threads to start (0 is guess)" },
#endif
{ "-npme", FALSE, etINT, {&npme},
"Number of separate nodes to be used for PME, -1 is guess" },
{ "-ddorder", FALSE, etENUM, {ddno_opt},
"DD node order" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
"Check for all bonded interactions with DD" },
{ "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
{ "-rdd", FALSE, etREAL, {&rdd},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
{ "-rcon", FALSE, etREAL, {&rconstr},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
{ "-dlb", FALSE, etENUM, {dddlb_opt},
"Dynamic load balancing (with DD)" },
{ "-dds", FALSE, etREAL, {&dlb_scale},
"Minimum allowed dlb scaling of the DD cell size" },
{ "-ddcsx", FALSE, etSTR, {&ddcsx},
"HIDDENThe DD cell sizes in x" },
{ "-ddcsy", FALSE, etSTR, {&ddcsy},
"HIDDENThe DD cell sizes in y" },
{ "-ddcsz", FALSE, etSTR, {&ddcsz},
"HIDDENThe DD cell sizes in z" },
{ "-gcom", FALSE, etINT,{&nstglobalcomm},
"Global communication frequency" },
{ "-v", FALSE, etBOOL,{&bVerbose},
"Be loud and noisy" },
{ "-compact", FALSE, etBOOL,{&bCompact},
"Write a compact log file" },
{ "-seppot", FALSE, etBOOL, {&bSepPot},
"Write separate V and dVdl terms for each interaction type and node to the log file(s)" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL,{&bReproducible},
"Try to avoid optimizations that affect binary reproducibility" },
{ "-cpt", FALSE, etREAL, {&cpt_period},
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT,{&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
"Attempt replica exchange every # steps" },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-ionize", FALSE, etBOOL,{&bIonize},
"Do a simulation including the effect of an X-Ray bombardment on your system" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining runtime" },
{ "-resetstep", FALSE, etINT, {&resetstep},
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
#ifdef GMX_OPENMM
,
{ "-device", FALSE, etSTR, {&deviceOptions},
"Device option string" }
#endif
};
gmx_edsam_t ed;
unsigned long Flags, PCA_Flags;
ivec ddxyz;
int dd_node_order;
gmx_bool bAddPart;
FILE *fplog,*fptest;
int sim_part,sim_part_fn;
const char *part_suffix=".part";
char suffix[STRLEN];
int rc;
char **multidir=NULL;
cr = init_par(&argc,&argv);
if (MASTER(cr))
CopyRight(stderr, argv[0]);
PCA_Flags = (PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_CAN_SET_DEFFNM
| (MASTER(cr) ? 0 : PCA_QUIET));
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
* also comment out the version of init_forcerec in md.c
* with NULL instead of opt2fn
*/
/*
if (!MASTER(cr))
{
PCA_Flags |= PCA_NOT_READ_NODE;
}
*/
parse_common_args(&argc,argv,PCA_Flags, NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL, &oenv);
/* we set these early because they might be used in init_multisystem()
Note that there is the potential for npme>nnodes until the number of
threads is set later on, if there's thread parallelization. That shouldn't
lead to problems. */
dd_node_order = nenum(ddno_opt);
cr->npmenodes = npme;
#ifndef GMX_THREADS
nthreads=1;
#endif
/* now check the -multi and -multidir option */
if (opt2bSet("-multidir", NFILE, fnm))
{
int i;
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
}
if (repl_ex_nst != 0 && nmultisim < 2)
gmx_fatal(FARGS,"Need at least two replicas for replica exchange (option -multi)");
if (nmultisim > 1) {
#ifndef GMX_THREADS
gmx_bool bParFn = (multidir == NULL);
init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
#else
gmx_fatal(FARGS,"mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support");
#endif
}
bAddPart = !bAppendFiles;
/* Check if there is ANY checkpoint file available */
sim_part = 1;
sim_part_fn = sim_part;
if (opt2bSet("-cpi",NFILE,fnm))
{
if (bSepPot && bAppendFiles)
{
gmx_fatal(FARGS,"Output file appending is not supported with -seppot");
}
bAppendFiles =
read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
fnm,cr),
&sim_part_fn,NULL,cr,
bAppendFiles,NFILE,fnm,
part_suffix,&bAddPart);
if (sim_part_fn==0 && MASTER(cr))
{
fprintf(stdout,"No previous checkpoint file present, assuming this is a new run.\n");
}
else
{
sim_part = sim_part_fn + 1;
}
if (MULTISIM(cr) && MASTER(cr))
{
check_multi_int(stdout,cr->ms,sim_part,"simulation part");
}
}
else
{
bAppendFiles = FALSE;
}
if (!bAppendFiles)
{
sim_part_fn = sim_part;
}
if (bAddPart)
{
/* Rename all output files (except checkpoint files) */
/* create new part name first (zero-filled) */
sprintf(suffix,"%s%04d",part_suffix,sim_part_fn);
add_suffix_to_output_names(fnm,NFILE,suffix);
if (MASTER(cr))
{
fprintf(stdout,"Checkpoint file is from part %d, new output files will be suffixed '%s'.\n",sim_part-1,suffix);
}
}
Flags = opt2bSet("-rerun",NFILE,fnm) ? MD_RERUN : 0;
Flags = Flags | (opt2bSet("-mmcg",NFILE,fnm) ? MD_MMCG : 0);
Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
Flags = Flags | (bIonize ? MD_IONIZE : 0);
Flags = Flags | (bPartDec ? MD_PARTDEC : 0);
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (sim_part>1 ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
Flags = Flags | (opt2bSet("-wpot",NFILE,fnm) ? MD_WALLPOT : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
if ((MASTER(cr) || bSepPot) && !bAppendFiles)
{
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,!bSepPot,Flags,&fplog);
CopyRight(fplog,argv[0]);
please_cite(fplog,"Hess2008b");
please_cite(fplog,"Spoel2005a");
please_cite(fplog,"Lindahl2001a");
please_cite(fplog,"Berendsen95a");
}
else if (!MASTER(cr) && bSepPot)
{
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,!bSepPot,Flags,&fplog);
}
else
{
fplog = NULL;
}
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
rc = mdrunner(nthreads, fplog,cr,NFILE,fnm,oenv,bVerbose,bCompact,
nstglobalcomm, ddxyz,dd_node_order,rdd,rconstr,
dddlb_opt[0],dlb_scale,ddcsx,ddcsy,ddcsz,
nstepout,resetstep,nmultisim,repl_ex_nst,repl_ex_seed,
pforce, cpt_period,max_hours,deviceOptions,Flags);
if (gmx_parallel_env_initialized())
gmx_finalize();
if (MULTIMASTER(cr)) {
thanx(stderr);
}
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bAppendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
int gmx_bundle(int argc,char *argv[])
{
const char *desc[] = {
"g_bundle analyzes bundles of axes. The axes can be for instance",
"helix axes. The program reads two index groups and divides both",
"of them in [TT]-na[tt] parts. The centers of mass of these parts",
"define the tops and bottoms of the axes.",
"Several quantities are written to file:",
"the axis length, the distance and the z-shift of the axis mid-points",
"with respect to the average center of all axes, the total tilt,",
"the radial tilt and the lateral tilt with respect to the average axis.",
"[PAR]",
"With options [TT]-ok[tt], [TT]-okr[tt] and [TT]-okl[tt] the total,",
"radial and lateral kinks of the axes are plotted. An extra index",
"group of kink atoms is required, which is also divided into [TT]-na[tt]",
"parts. The kink angle is defined as the angle between the kink-top and",
"the bottom-kink vectors.",
"[PAR]",
"With option [TT]-oa[tt] the top, mid (or kink when [TT]-ok[tt] is set)",
"and bottom points of each axis",
"are written to a pdb file each frame. The residue numbers correspond",
"to the axis numbers. When viewing this file with [TT]rasmol[tt], use the",
"command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
"display the reference axis."
};
static int n=0;
static gmx_bool bZ=FALSE;
t_pargs pa[] = {
{ "-na", FALSE, etINT, {&n},
"Number of axes" },
{ "-z", FALSE, etBOOL, {&bZ},
"Use the Z-axis as reference iso the average axis" }
};
FILE *out,*flen,*fdist,*fz,*ftilt,*ftiltr,*ftiltl;
FILE *fkink=NULL,*fkinkr=NULL,*fkinkl=NULL;
t_trxstatus *status;
t_trxstatus *fpdb;
t_topology top;
int ePBC;
rvec *xtop;
matrix box;
t_trxframe fr;
t_atoms outatoms;
real t,comp;
int natoms;
char *grpname[MAX_ENDS],title[256];
/* FIXME: The constness should not be cast away */
char *anm=(char *)"CA",*rnm=(char *)"GLY";
int i,j,gnx[MAX_ENDS];
atom_id *index[MAX_ENDS];
t_bundle bun;
gmx_bool bKink;
rvec va,vb,vc,vr,vl;
output_env_t oenv;
gmx_rmpbc_t gpbc=NULL;
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-ol", "bun_len", ffWRITE },
{ efXVG, "-od", "bun_dist", ffWRITE },
{ efXVG, "-oz", "bun_z", ffWRITE },
{ efXVG, "-ot", "bun_tilt", ffWRITE },
{ efXVG, "-otr", "bun_tiltr", ffWRITE },
{ efXVG, "-otl", "bun_tiltl", ffWRITE },
{ efXVG, "-ok", "bun_kink", ffOPTWR },
{ efXVG, "-okr", "bun_kinkr", ffOPTWR },
{ efXVG, "-okl", "bun_kinkl", ffOPTWR },
{ efPDB, "-oa", "axes", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,TRUE);
bKink = opt2bSet("-ok",NFILE,fnm) || opt2bSet("-okr",NFILE,fnm)
|| opt2bSet("-okl",NFILE,fnm);
if (bKink)
bun.nend = 3;
else
bun.nend = 2;
fprintf(stderr,"Select a group of top and a group of bottom ");
if (bKink)
fprintf(stderr,"and a group of kink ");
fprintf(stderr,"atoms\n");
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),bun.nend,
gnx,index,grpname);
if (n<=0 || gnx[0] % n || gnx[1] % n || (bKink && gnx[2] % n))
gmx_fatal(FARGS,
"The size of one of your index groups is not a multiple of n");
bun.n = n;
snew(bun.end[0],n);
snew(bun.end[1],n);
if (bKink)
snew(bun.end[2],n);
snew(bun.mid,n);
snew(bun.dir,n);
snew(bun.len,n);
flen = xvgropen(opt2fn("-ol",NFILE,fnm),"Axis lengths",
output_env_get_xvgr_tlabel(oenv),"(nm)",oenv);
fdist = xvgropen(opt2fn("-od",NFILE,fnm),"Distance of axis centers",
output_env_get_xvgr_tlabel(oenv),"(nm)",oenv);
fz = xvgropen(opt2fn("-oz",NFILE,fnm),"Z-shift of axis centers",
output_env_get_xvgr_tlabel(oenv),"(nm)",oenv);
ftilt = xvgropen(opt2fn("-ot",NFILE,fnm),"Axis tilts",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
ftiltr = xvgropen(opt2fn("-otr",NFILE,fnm),"Radial axis tilts",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
ftiltl = xvgropen(opt2fn("-otl",NFILE,fnm),"Lateral axis tilts",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
if (bKink) {
fkink = xvgropen(opt2fn("-ok",NFILE,fnm),"Kink angles",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
fkinkr = xvgropen(opt2fn("-okr",NFILE,fnm),"Radial kink angles",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
if (output_env_get_print_xvgr_codes(oenv))
fprintf(fkinkr,"@ subtitle \"+ = ) ( - = ( )\"\n");
fkinkl = xvgropen(opt2fn("-okl",NFILE,fnm),"Lateral kink angles",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
}
if (opt2bSet("-oa",NFILE,fnm)) {
init_t_atoms(&outatoms,3*n,FALSE);
outatoms.nr = 3*n;
for(i=0; i<3*n; i++) {
outatoms.atomname[i] = &anm;
outatoms.atom[i].resind = i/3;
outatoms.resinfo[i/3].name = &rnm;
outatoms.resinfo[i/3].nr = i/3 + 1;
outatoms.resinfo[i/3].ic = ' ';
}
fpdb = open_trx(opt2fn("-oa",NFILE,fnm),"w");
} else
fpdb = NULL;
read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_NEED_X);
gpbc = gmx_rmpbc_init(&top.idef,ePBC,fr.natoms,fr.box);
do {
gmx_rmpbc_trxfr(gpbc,&fr);
calc_axes(fr.x,top.atoms.atom,gnx,index,!bZ,&bun);
t = output_env_conv_time(oenv,fr.time);
fprintf(flen," %10g",t);
fprintf(fdist," %10g",t);
fprintf(fz," %10g",t);
fprintf(ftilt," %10g",t);
fprintf(ftiltr," %10g",t);
fprintf(ftiltl," %10g",t);
if (bKink) {
fprintf(fkink," %10g",t);
fprintf(fkinkr," %10g",t);
fprintf(fkinkl," %10g",t);
}
for(i=0; i<bun.n; i++) {
fprintf(flen," %6g",bun.len[i]);
fprintf(fdist," %6g",norm(bun.mid[i]));
fprintf(fz," %6g",bun.mid[i][ZZ]);
fprintf(ftilt," %6g",RAD2DEG*acos(bun.dir[i][ZZ]));
comp = bun.mid[i][XX]*bun.dir[i][XX]+bun.mid[i][YY]*bun.dir[i][YY];
fprintf(ftiltr," %6g",RAD2DEG*
asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
comp = bun.mid[i][YY]*bun.dir[i][XX]-bun.mid[i][XX]*bun.dir[i][YY];
fprintf(ftiltl," %6g",RAD2DEG*
asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
if (bKink) {
rvec_sub(bun.end[0][i],bun.end[2][i],va);
rvec_sub(bun.end[2][i],bun.end[1][i],vb);
unitv_no_table(va,va);
unitv_no_table(vb,vb);
fprintf(fkink," %6g",RAD2DEG*acos(iprod(va,vb)));
cprod(va,vb,vc);
copy_rvec(bun.mid[i],vr);
vr[ZZ] = 0;
unitv_no_table(vr,vr);
fprintf(fkinkr," %6g",RAD2DEG*asin(iprod(vc,vr)));
vl[XX] = vr[YY];
vl[YY] = -vr[XX];
vl[ZZ] = 0;
fprintf(fkinkl," %6g",RAD2DEG*asin(iprod(vc,vl)));
}
}
fprintf(flen,"\n");
fprintf(fdist,"\n");
fprintf(fz,"\n");
fprintf(ftilt,"\n");
fprintf(ftiltr,"\n");
fprintf(ftiltl,"\n");
if (bKink) {
fprintf(fkink,"\n");
fprintf(fkinkr,"\n");
fprintf(fkinkl,"\n");
}
if (fpdb )
dump_axes(fpdb,&fr,&outatoms,&bun);
} while(read_next_frame(oenv,status,&fr));
gmx_rmpbc_done(gpbc);
close_trx(status);
if (fpdb )
close_trx(fpdb);
ffclose(flen);
ffclose(fdist);
ffclose(fz);
ffclose(ftilt);
ffclose(ftiltr);
ffclose(ftiltl);
if (bKink) {
ffclose(fkink);
ffclose(fkinkr);
ffclose(fkinkl);
}
thanx(stderr);
return 0;
}
int gmx_genbox(int argc, char *argv[])
{
const char *desc[] = {
"[TT]genbox[tt] can do one of 3 things:[PAR]",
"1) Generate a box of solvent. Specify [TT]-cs[tt] and [TT]-box[tt]. Or specify [TT]-cs[tt] and",
"[TT]-cp[tt] with a structure file with a box, but without atoms.[PAR]",
"2) Solvate a solute configuration, e.g. a protein, in a bath of solvent ",
"molecules. Specify [TT]-cp[tt] (solute) and [TT]-cs[tt] (solvent). ",
"The box specified in the solute coordinate file ([TT]-cp[tt]) is used,",
"unless [TT]-box[tt] is set.",
"If you want the solute to be centered in the box,",
"the program [TT]editconf[tt] has sophisticated options",
"to change the box dimensions and center the solute.",
"Solvent molecules are removed from the box where the ",
"distance between any atom of the solute molecule(s) and any atom of ",
"the solvent molecule is less than the sum of the van der Waals radii of ",
"both atoms. A database ([TT]vdwradii.dat[tt]) of van der Waals radii is ",
"read by the program, and atoms not in the database are ",
"assigned a default distance [TT]-vdwd[tt].",
"Note that this option will also influence the distances between",
"solvent molecules if they contain atoms that are not in the database.",
"[PAR]",
"3) Insert a number ([TT]-nmol[tt]) of extra molecules ([TT]-ci[tt]) ",
"at random positions.",
"The program iterates until [TT]nmol[tt] molecules",
"have been inserted in the box. To test whether an insertion is ",
"successful the same van der Waals criterium is used as for removal of ",
"solvent molecules. When no appropriately-sized ",
"holes (holes that can hold an extra molecule) are available, the ",
"program tries for [TT]-nmol[tt] * [TT]-try[tt] times before giving up. ",
"Increase [TT]-try[tt] if you have several small holes to fill.[PAR]",
"If you need to do more than one of the above operations, it can be",
"best to call [TT]genbox[tt] separately for each operation, so that",
"you are sure of the order in which the operations occur.[PAR]",
"The default solvent is Simple Point Charge water (SPC), with coordinates ",
"from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
"for other 3-site water models, since a short equibilibration will remove",
"the small differences between the models.",
"Other solvents are also supported, as well as mixed solvents. The",
"only restriction to solvent types is that a solvent molecule consists",
"of exactly one residue. The residue information in the coordinate",
"files is used, and should therefore be more or less consistent.",
"In practice this means that two subsequent solvent molecules in the ",
"solvent coordinate file should have different residue number.",
"The box of solute is built by stacking the coordinates read from",
"the coordinate file. This means that these coordinates should be ",
"equlibrated in periodic boundary conditions to ensure a good",
"alignment of molecules on the stacking interfaces.",
"The [TT]-maxsol[tt] option simply adds only the first [TT]-maxsol[tt]",
"solvent molecules and leaves out the rest that would have fitted",
"into the box. This can create a void that can cause problems later.",
"Choose your volume wisely.[PAR]",
"The program can optionally rotate the solute molecule to align the",
"longest molecule axis along a box edge. This way the amount of solvent",
"molecules necessary is reduced.",
"It should be kept in mind that this only works for",
"short simulations, as e.g. an alpha-helical peptide in solution can ",
"rotate over 90 degrees, within 500 ps. In general it is therefore ",
"better to make a more or less cubic box.[PAR]",
"Setting [TT]-shell[tt] larger than zero will place a layer of water of",
"the specified thickness (nm) around the solute. Hint: it is a good",
"idea to put the protein in the center of a box first (using [TT]editconf[tt]).",
"[PAR]",
"Finally, [TT]genbox[tt] will optionally remove lines from your topology file in ",
"which a number of solvent molecules is already added, and adds a ",
"line with the total number of solvent molecules in your coordinate file."
};
const char *bugs[] = {
"Molecules must be whole in the initial configurations.",
};
/* parameter data */
gmx_bool bSol, bProt, bBox;
const char *conf_prot, *confout;
int bInsert;
real *r;
char *title_ins;
gmx_atomprop_t aps;
/* protein configuration data */
char *title = NULL;
t_atoms atoms;
rvec *x, *v = NULL;
int ePBC = -1;
matrix box;
t_pbc pbc;
/* other data types */
int atoms_added, residues_added;
t_filenm fnm[] = {
{ efSTX, "-cp", "protein", ffOPTRD },
{ efSTX, "-cs", "spc216", ffLIBOPTRD},
{ efSTX, "-ci", "insert", ffOPTRD},
{ efSTO, NULL, NULL, ffWRITE},
{ efTOP, NULL, NULL, ffOPTRW},
};
#define NFILE asize(fnm)
static int nmol_ins = 0, nmol_try = 10, seed = 1997;
static real r_distance = 0.105, r_shell = 0;
static rvec new_box = {0.0, 0.0, 0.0};
static gmx_bool bReadV = FALSE;
static int max_sol = 0;
output_env_t oenv;
t_pargs pa[] = {
{ "-box", FALSE, etRVEC, {new_box},
"Box size" },
{ "-nmol", FALSE, etINT, {&nmol_ins},
"Number of extra molecules to insert" },
{ "-try", FALSE, etINT, {&nmol_try},
"Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
{ "-seed", FALSE, etINT, {&seed},
"Random generator seed"},
{ "-vdwd", FALSE, etREAL, {&r_distance},
"Default van der Waals distance"},
{ "-shell", FALSE, etREAL, {&r_shell},
"Thickness of optional water layer around solute" },
{ "-maxsol", FALSE, etINT, {&max_sol},
"Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored" },
{ "-vel", FALSE, etBOOL, {&bReadV},
"Keep velocities from input solute and solvent" }
};
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
bInsert = opt2bSet("-ci", NFILE, fnm) && (nmol_ins > 0);
bSol = opt2bSet("-cs", NFILE, fnm);
bProt = opt2bSet("-cp", NFILE, fnm);
bBox = opt2parg_bSet("-box", asize(pa), pa);
/* check input */
if (bInsert && nmol_ins <= 0)
{
gmx_fatal(FARGS, "When specifying inserted molecules (-ci), "
"-nmol must be larger than 0");
}
if (!bInsert && nmol_ins > 0)
{
gmx_fatal(FARGS,
"You tried to insert molecules with -nmol, but did not supply "
"a molecule to insert with -ci.");
}
if (!bProt && !bBox)
{
gmx_fatal(FARGS, "When no solute (-cp) is specified, "
"a box size (-box) must be specified");
}
aps = gmx_atomprop_init();
if (bProt)
{
/*generate a solute configuration */
conf_prot = opt2fn("-cp", NFILE, fnm);
title = read_prot(conf_prot, &atoms, &x, bReadV ? &v : NULL, &r, &ePBC, box,
aps, r_distance);
if (bReadV && !v)
{
fprintf(stderr, "Note: no velocities found\n");
}
if (atoms.nr == 0)
{
fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
bProt = FALSE;
}
}
if (!bProt)
{
atoms.nr = 0;
atoms.nres = 0;
atoms.resinfo = NULL;
atoms.atomname = NULL;
atoms.atom = NULL;
atoms.pdbinfo = NULL;
x = NULL;
r = NULL;
}
if (bBox)
{
ePBC = epbcXYZ;
clear_mat(box);
box[XX][XX] = new_box[XX];
box[YY][YY] = new_box[YY];
box[ZZ][ZZ] = new_box[ZZ];
}
if (det(box) == 0)
{
gmx_fatal(FARGS, "Undefined solute box.\nCreate one with editconf "
"or give explicit -box command line option");
}
/* add nmol_ins molecules of atoms_ins
in random orientation at random place */
if (bInsert)
{
title_ins = insert_mols(opt2fn("-ci", NFILE, fnm), nmol_ins, nmol_try, seed,
&atoms, &x, &r, ePBC, box, aps, r_distance, r_shell,
oenv);
}
else
{
title_ins = strdup("Generated by genbox");
}
/* add solvent */
if (bSol)
{
add_solv(opt2fn("-cs", NFILE, fnm), &atoms, &x, v ? &v : NULL, &r, ePBC, box,
aps, r_distance, &atoms_added, &residues_added, r_shell, max_sol,
oenv);
}
/* write new configuration 1 to file confout */
confout = ftp2fn(efSTO, NFILE, fnm);
fprintf(stderr, "Writing generated configuration to %s\n", confout);
if (bProt)
{
write_sto_conf(confout, title, &atoms, x, v, ePBC, box);
/* print box sizes and box type to stderr */
fprintf(stderr, "%s\n", title);
}
else
{
write_sto_conf(confout, title_ins, &atoms, x, v, ePBC, box);
}
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
atoms.nr, atoms.nres);
update_top(&atoms, box, NFILE, fnm, aps);
gmx_atomprop_destroy(aps);
thanx(stderr);
return 0;
}
int gmx_dist(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_dist[tt] can calculate the distance between the centers of mass of two",
"groups of atoms as a function of time. The total distance and its",
"[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-components are plotted.[PAR]",
"Or when [TT]-dist[tt] is set, print all the atoms in group 2 that are",
"closer than a certain distance to the center of mass of group 1.[PAR]",
"With options [TT]-lt[tt] and [TT]-dist[tt] the number of contacts",
"of all atoms in group 2 that are closer than a certain distance",
"to the center of mass of group 1 are plotted as a function of the time",
"that the contact was continuously present.[PAR]",
"Other programs that calculate distances are [TT]g_mindist[tt]",
"and [TT]g_bond[tt]."
};
t_topology *top=NULL;
int ePBC;
real t,t0,cut2,dist2;
rvec *x=NULL,*v=NULL,dx;
matrix box;
t_trxstatus *status;
int natoms;
int g,d,i,j,res,teller=0;
atom_id aid;
int ngrps; /* the number of index groups */
atom_id **index,max; /* the index for the atom numbers */
int *isize; /* the size of each group */
char **grpname; /* the name of each group */
rvec *com;
real *mass;
FILE *fp=NULL,*fplt=NULL;
gmx_bool bCutoff,bPrintDist,bLifeTime;
t_pbc *pbc;
int *contact_time=NULL,*ccount=NULL,ccount_nalloc=0,sum;
char buf[STRLEN];
output_env_t oenv;
gmx_rmpbc_t gpbc=NULL;
const char *leg[4] = { "|d|","d\\sx\\N","d\\sy\\N","d\\sz\\N" };
static real cut=0;
static t_pargs pa[] = {
{ "-dist", FALSE, etREAL, {&cut},
"Print all atoms in group 2 closer than dist to the center of mass of group 1" }
};
#define NPA asize(pa)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPX, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "dist", ffOPTWR },
{ efXVG, "-lt", "lifetime", ffOPTWR },
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL,&oenv);
bCutoff = opt2parg_bSet("-dist",NPA,pa);
cut2 = cut*cut;
bLifeTime = opt2bSet("-lt",NFILE,fnm);
bPrintDist = (bCutoff && !bLifeTime);
top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
/* read index files */
ngrps = 2;
snew(com,ngrps);
snew(grpname,ngrps);
snew(index,ngrps);
snew(isize,ngrps);
get_index(&top->atoms,ftp2fn(efNDX,NFILE,fnm),ngrps,isize,index,grpname);
/* calculate mass */
max=0;
snew(mass,ngrps);
for(g=0;(g<ngrps);g++) {
mass[g]=0;
for(i=0;(i<isize[g]);i++) {
if (index[g][i]>max)
max=index[g][i];
if (index[g][i] >= top->atoms.nr)
gmx_fatal(FARGS,"Atom number %d, item %d of group %d, is larger than number of atoms in the topolgy (%d)\n",index[g][i]+1,i+1,g+1,top->atoms.nr+1);
mass[g]+=top->atoms.atom[index[g][i]].m;
}
}
natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
t0 = t;
if (max>=natoms)
gmx_fatal(FARGS,"Atom number %d in an index group is larger than number of atoms in the trajectory (%d)\n",(int)max+1,natoms);
if (!bCutoff) {
/* open output file */
fp = xvgropen(ftp2fn(efXVG,NFILE,fnm),
"Distance","Time (ps)","Distance (nm)",oenv);
xvgr_legend(fp,4,leg,oenv);
} else {
ngrps = 1;
if (bLifeTime)
snew(contact_time,isize[1]);
}
if (ePBC != epbcNONE)
snew(pbc,1);
else
pbc = NULL;
gpbc = gmx_rmpbc_init(&top->idef,ePBC,natoms,box);
do {
/* initialisation for correct distance calculations */
if (pbc) {
set_pbc(pbc,ePBC,box);
/* make molecules whole again */
gmx_rmpbc(gpbc,natoms,box,x);
}
/* calculate center of masses */
for(g=0;(g<ngrps);g++) {
if (isize[g] == 1) {
copy_rvec(x[index[g][0]],com[g]);
} else {
for(d=0;(d<DIM);d++) {
com[g][d]=0;
for(i=0;(i<isize[g]);i++) {
com[g][d] += x[index[g][i]][d] * top->atoms.atom[index[g][i]].m;
}
com[g][d] /= mass[g];
}
}
}
if (!bCutoff) {
/* write to output */
fprintf(fp,"%12.7f ",t);
for(g=0;(g<ngrps/2);g++) {
if (pbc)
pbc_dx(pbc,com[2*g],com[2*g+1],dx);
else
rvec_sub(com[2*g],com[2*g+1],dx);
fprintf(fp,"%12.7f %12.7f %12.7f %12.7f",
norm(dx),dx[XX],dx[YY],dx[ZZ]);
}
fprintf(fp,"\n");
} else {
for(i=0;(i<isize[1]);i++) {
j=index[1][i];
if (pbc)
pbc_dx(pbc,x[j],com[0],dx);
else
rvec_sub(x[j],com[0],dx);
dist2 = norm2(dx);
if (dist2<cut2) {
if (bPrintDist) {
res=top->atoms.atom[j].resind;
fprintf(stdout,"\rt: %g %d %s %d %s %g (nm)\n",
t,top->atoms.resinfo[res].nr,*top->atoms.resinfo[res].name,
j+1,*top->atoms.atomname[j],sqrt(dist2));
}
if (bLifeTime)
contact_time[i]++;
} else {
if (bLifeTime) {
if (contact_time[i]) {
add_contact_time(&ccount,&ccount_nalloc,contact_time[i]-1);
contact_time[i] = 0;
}
}
}
}
}
teller++;
} while (read_next_x(oenv,status,&t,natoms,x,box));
gmx_rmpbc_done(gpbc);
if (!bCutoff)
ffclose(fp);
close_trj(status);
if (bCutoff && bLifeTime) {
/* Add the contacts still present in the last frame */
for(i=0; i<isize[1]; i++)
if (contact_time[i])
add_contact_time(&ccount,&ccount_nalloc,contact_time[i]-1);
sprintf(buf,"%s - %s within %g nm",
grpname[0],grpname[1],cut);
fp = xvgropen(opt2fn("-lt",NFILE,fnm),
buf,"Time (ps)","Number of contacts",oenv);
for(i=0; i<min(ccount_nalloc,teller-1); i++) {
/* Account for all subintervals of longer intervals */
sum = 0;
for(j=i; j<ccount_nalloc; j++)
sum += (j-i+1)*ccount[j];
fprintf(fp,"%10.3f %10.3f\n",i*(t-t0)/(teller-1),sum/(double)(teller-i));
}
ffclose(fp);
}
thanx(stderr);
return 0;
}
