static void make_dist_leg(FILE *fp,int gnx,atom_id index[],t_atoms *atoms)
{
char **leg;
int i;
snew(leg,gnx/2);
for(i=0; i<gnx; i+=2) {
snew(leg[i/2],256);
sprintf(leg[i/2],"%s %s%d - %s %s%d",
*(atoms->atomname[index[i]]),
*(atoms->resname[atoms->atom[index[i]].resnr]),
atoms->atom[index[i]].resnr+1,
*(atoms->atomname[index[i+1]]),
*(atoms->resname[atoms->atom[index[i+1]].resnr]),
atoms->atom[index[i+1]].resnr+1);
}
xvgr_legend(fp,gnx/2,leg);
for(i=0; i<gnx/2; i++)
sfree(leg[i]);
sfree(leg);
}
void dump_ana_ener(t_ana_ener *ae,int nsim,real dt,char *edump,
t_ana_struct *total)
{
FILE *fp;
int i,j;
real fac;
fac = 1.0/(nsim*ELECTRONVOLT);
fp=xvgropen(edump,"Energies","Time (fs)","E (eV)");
xvgr_legend(fp,eNR,enms);
fprintf(fp,"@ s%d legend \"Ek/Nelec\"\n",eNR);
fprintf(fp,"@ type nxy\n");
for(i=0; (i<ae->nx); i++) {
fprintf(fp,"%10f",1000.0*dt*i);
for(j=0; (j<eNR); j++)
fprintf(fp," %8.3f",ae->e[i][j]*fac);
fprintf(fp," %8.3f\n",ae->e[i][eELECTRON]/(ELECTRONVOLT*total->nion[i]));
}
fprintf(fp,"&\n");
ffclose(fp);
}
void write_xvg(const char *fn, const char *title, int nx, int ny, real **y,
const char **leg, const output_env_t oenv)
{
FILE *fp;
int i, j;
fp = xvgropen(fn, title, "X", "Y", oenv);
if (leg)
{
xvgr_legend(fp, ny-1, leg, oenv);
}
for (i = 0; (i < nx); i++)
{
for (j = 0; (j < ny); j++)
{
fprintf(fp, " %12.5e", y[j][i]);
}
fprintf(fp, "\n");
}
xvgrclose(fp);
}
static void pr_dev(t_coupl_rec *tcr,
real t,real dev[eoObsNR],t_commrec *cr,int nfile,t_filenm fnm[])
{
static FILE *fp=NULL;
char **ptr;
int i,j;
if (!fp) {
fp=xvgropen(opt2fn("-devout",nfile,fnm),
"Deviations from target value","Time (ps)","");
snew(ptr,eoObsNR);
for(i=j=0; (i<eoObsNR); i++)
if (tcr->bObsUsed[i])
ptr[j++] = eoNames[i];
xvgr_legend(fp,j,ptr);
sfree(ptr);
}
fprintf(fp,"%10.3f",t);
for(i=0; (i<eoObsNR); i++)
if (tcr->bObsUsed[i])
fprintf(fp," %10.3e",dev[i]);
fprintf(fp,"\n");
fflush(fp);
}
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_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_mdmat(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] 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 [gmx-xpm2ps] 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 = {{0}};
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
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);
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, x, box));
fprintf(stderr, "\n");
close_trj(status);
gmx_rmpbc_done(gpbc);
if (bFrames)
{
gmx_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)
{
char **legend;
snew(legend, 5);
for (i = 0; i < 5; i++)
{
snew(legend[i], STRLEN);
}
tot_nmat(nres, natoms, nframes, totnmat, tot_n, mean_n);
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Increase in number of contacts", "Residue", "Ratio", oenv);
sprintf(legend[0], "Total/mean");
sprintf(legend[1], "Total");
sprintf(legend[2], "Mean");
sprintf(legend[3], "# atoms");
sprintf(legend[4], "Mean/# atoms");
xvgr_legend(fp, 5, (const char**)legend, oenv);
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]);
}
xvgrclose(fp);
}
return 0;
}
int gmx_dos(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the Density of States from a simulations.",
"In order for this to be meaningful the velocities must be saved",
"in the trajecotry with sufficiently high frequency such as to cover",
"all vibrations. For flexible systems that would be around a few fs",
"between saving. Properties based on the DoS are printed on the",
"standard output."
"Note that the density of states is calculated from the mass-weighted",
"autocorrelation, and by default only from the square of the real",
"component rather than absolute value. This means the shape can differ",
"substantially from the plain vibrational power spectrum you can",
"calculate with gmx velacc."
};
const char *bugs[] = {
"This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision)."
};
FILE *fp, *fplog;
t_topology top;
int ePBC = -1;
t_trxframe fr;
matrix box;
int gnx;
real t0, t1;
t_trxstatus *status;
int nV, nframes, n_alloc, i, j, fftcode, Nmol, Natom;
double rho, dt, Vsum, V, tmass, dostot, dos2;
real **c1, **dos, mi, beta, bfac, *nu, *tt, stddev, c1j;
gmx_output_env_t *oenv;
gmx_fft_t fft;
double cP, DiffCoeff, Delta, f, y, z, sigHS, Shs, Sig, DoS0, recip_fac;
double wCdiff, wSdiff, wAdiff, wEdiff;
int grpNatoms;
int *index;
char *grpname;
double invNormalize;
gmx_bool normalizeAutocorrelation;
static gmx_bool bVerbose = TRUE, bAbsolute = FALSE, bNormalizeDos = FALSE;
static gmx_bool bRecip = FALSE;
static real Temp = 298.15, toler = 1e-6;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy."
},
{ "-recip", FALSE, etBOOL, {&bRecip},
"Use cm^-1 on X-axis instead of 1/ps for DoS plots."
},
{ "-abs", FALSE, etBOOL, {&bAbsolute},
"Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only"
},
{ "-normdos", FALSE, etBOOL, {&bNormalizeDos},
"Normalize the DoS such that it adds up to 3N. This should usually not be necessary."
},
{ "-T", FALSE, etREAL, {&Temp},
"Temperature in the simulation"
},
{ "-toler", FALSE, etREAL, {&toler},
"[HIDDEN]Tolerance when computing the fluidicity using bisection algorithm"
}
};
t_filenm fnm[] = {
{ efTRN, "-f", NULL, ffREAD },
{ efTPR, "-s", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-vacf", "vacf", ffWRITE },
{ efXVG, "-mvacf", "mvacf", ffWRITE },
{ efXVG, "-dos", "dos", ffWRITE },
{ efLOG, "-g", "dos", ffWRITE },
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
const char *DoSlegend[] = {
"DoS(v)", "DoS(v)[Solid]", "DoS(v)[Diff]"
};
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,
asize(bugs), bugs, &oenv))
{
return 0;
}
beta = 1/(Temp*BOLTZ);
fplog = gmx_fio_fopen(ftp2fn(efLOG, NFILE, fnm), "w");
fprintf(fplog, "Doing density of states analysis based on trajectory.\n");
please_cite(fplog, "Pascal2011a");
please_cite(fplog, "Caleman2011b");
read_tps_conf(ftp2fn(efTPR, NFILE, fnm), &top, &ePBC, NULL, NULL, box, TRUE);
/* Handle index groups */
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &grpNatoms, &index, &grpname);
V = det(box);
tmass = 0;
for (i = 0; i < grpNatoms; i++)
{
tmass += top.atoms.atom[index[i]].m;
}
Natom = grpNatoms;
Nmol = calcMoleculesInIndexGroup(&top.mols, top.atoms.nr, index, grpNatoms);
gnx = Natom*DIM;
/* 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;
nframes = 0;
Vsum = 0;
nV = 0;
do
{
if (fr.bBox)
{
V = det(fr.box);
Vsum += V;
nV++;
}
if (nframes >= n_alloc)
{
n_alloc += 100;
for (i = 0; i < gnx; i++)
{
srenew(c1[i], n_alloc);
}
}
for (i = 0; i < gnx; i += DIM)
{
c1[i+XX][nframes] = fr.v[index[i/DIM]][XX];
c1[i+YY][nframes] = fr.v[index[i/DIM]][YY];
c1[i+ZZ][nframes] = fr.v[index[i/DIM]][ZZ];
}
t1 = fr.time;
nframes++;
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
dt = (t1-t0)/(nframes-1);
if (nV > 0)
{
V = Vsum/nV;
}
if (bVerbose)
{
printf("Going to do %d fourier transforms of length %d. Hang on.\n",
gnx, nframes);
}
/* Unfortunately the -normalize program option for the autocorrelation
* function calculation is added as a hack with a static variable in the
* autocorrelation.c source. That would work if we called the normal
* do_autocorr(), but this routine overrides that by directly calling
* the low-level functionality. That unfortunately leads to ignoring the
* default value for the option (which is to normalize).
* Since the absolute value seems to be important for the subsequent
* analysis below, we detect the value directly from the option, calculate
* the autocorrelation without normalization, and then apply the
* normalization just to the autocorrelation output
* (or not, if the user asked for a non-normalized autocorrelation).
*/
normalizeAutocorrelation = opt2parg_bool("-normalize", npargs, ppa);
/* Note that we always disable normalization here, regardless of user settings */
low_do_autocorr(NULL, oenv, NULL, nframes, gnx, nframes, c1, dt, eacNormal, 0, FALSE,
FALSE, FALSE, -1, -1, 0);
snew(dos, DOS_NR);
for (j = 0; (j < DOS_NR); j++)
{
snew(dos[j], nframes+4);
}
if (bVerbose)
{
printf("Going to merge the ACFs into the mass-weighted and plain ACF\n");
}
for (i = 0; (i < gnx); i += DIM)
{
mi = top.atoms.atom[index[i/DIM]].m;
for (j = 0; (j < nframes/2); j++)
{
c1j = (c1[i+XX][j] + c1[i+YY][j] + c1[i+ZZ][j]);
dos[VACF][j] += c1j/Natom;
dos[MVACF][j] += mi*c1j;
}
}
fp = xvgropen(opt2fn("-vacf", NFILE, fnm), "Velocity autocorrelation function",
"Time (ps)", "C(t)", oenv);
snew(tt, nframes/2);
invNormalize = normalizeAutocorrelation ? 1.0/dos[VACF][0] : 1.0;
for (j = 0; (j < nframes/2); j++)
{
tt[j] = j*dt;
fprintf(fp, "%10g %10g\n", tt[j], dos[VACF][j] * invNormalize);
}
xvgrclose(fp);
fp = xvgropen(opt2fn("-mvacf", NFILE, fnm), "Mass-weighted velocity autocorrelation function",
"Time (ps)", "C(t)", oenv);
invNormalize = normalizeAutocorrelation ? 1.0/dos[VACF][0] : 1.0;
for (j = 0; (j < nframes/2); j++)
{
fprintf(fp, "%10g %10g\n", tt[j], dos[MVACF][j] * invNormalize);
}
xvgrclose(fp);
if ((fftcode = gmx_fft_init_1d_real(&fft, nframes/2,
GMX_FFT_FLAG_NONE)) != 0)
{
gmx_fatal(FARGS, "gmx_fft_init_1d_real returned %d", fftcode);
}
if ((fftcode = gmx_fft_1d_real(fft, GMX_FFT_REAL_TO_COMPLEX,
(void *)dos[MVACF], (void *)dos[DOS])) != 0)
{
gmx_fatal(FARGS, "gmx_fft_1d_real returned %d", fftcode);
}
/* First compute the DoS */
/* Magic factor of 8 included now. */
bfac = 8*dt*beta/2;
dos2 = 0;
snew(nu, nframes/4);
for (j = 0; (j < nframes/4); j++)
{
nu[j] = 2*j/(t1-t0);
dos2 += gmx::square(dos[DOS][2*j]) + gmx::square(dos[DOS][2*j+1]);
if (bAbsolute)
{
dos[DOS][j] = bfac*std::hypot(dos[DOS][2*j], dos[DOS][2*j+1]);
}
else
{
dos[DOS][j] = bfac*dos[DOS][2*j];
}
}
/* Normalize it */
dostot = evaluate_integral(nframes/4, nu, dos[DOS], NULL, nframes/4, &stddev);
if (bNormalizeDos)
{
for (j = 0; (j < nframes/4); j++)
{
dos[DOS][j] *= 3*Natom/dostot;
}
}
/* Now analyze it */
DoS0 = dos[DOS][0];
/* Note this eqn. is incorrect in Pascal2011a! */
Delta = ((2*DoS0/(9*Natom))*std::sqrt(M_PI*BOLTZ*Temp*Natom/tmass)*
std::pow((Natom/V), 1.0/3.0)*std::pow(6.0/M_PI, 2.0/3.0));
f = calc_fluidicity(Delta, toler);
y = calc_y(f, Delta, toler);
z = calc_compress(y);
Sig = BOLTZ*(5.0/2.0+std::log(2*M_PI*BOLTZ*Temp/(gmx::square(PLANCK))*V/(f*Natom)));
Shs = Sig+calc_Shs(f, y);
rho = (tmass*AMU)/(V*NANO*NANO*NANO);
sigHS = std::cbrt(6*y*V/(M_PI*Natom));
fprintf(fplog, "System = \"%s\"\n", *top.name);
fprintf(fplog, "Nmol = %d\n", Nmol);
fprintf(fplog, "Natom = %d\n", Natom);
fprintf(fplog, "dt = %g ps\n", dt);
fprintf(fplog, "tmass = %g amu\n", tmass);
fprintf(fplog, "V = %g nm^3\n", V);
fprintf(fplog, "rho = %g g/l\n", rho);
fprintf(fplog, "T = %g K\n", Temp);
fprintf(fplog, "beta = %g mol/kJ\n", beta);
fprintf(fplog, "\nDoS parameters\n");
fprintf(fplog, "Delta = %g\n", Delta);
fprintf(fplog, "fluidicity = %g\n", f);
fprintf(fplog, "hard sphere packing fraction = %g\n", y);
fprintf(fplog, "hard sphere compressibility = %g\n", z);
fprintf(fplog, "ideal gas entropy = %g\n", Sig);
fprintf(fplog, "hard sphere entropy = %g\n", Shs);
fprintf(fplog, "sigma_HS = %g nm\n", sigHS);
fprintf(fplog, "DoS0 = %g\n", DoS0);
fprintf(fplog, "Dos2 = %g\n", dos2);
fprintf(fplog, "DoSTot = %g\n", dostot);
/* Now compute solid (2) and diffusive (3) components */
fp = xvgropen(opt2fn("-dos", NFILE, fnm), "Density of states",
bRecip ? "E (cm\\S-1\\N)" : "\\f{12}n\\f{4} (1/ps)",
"\\f{4}S(\\f{12}n\\f{4})", oenv);
xvgr_legend(fp, asize(DoSlegend), DoSlegend, oenv);
recip_fac = bRecip ? (1e7/SPEED_OF_LIGHT) : 1.0;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_DIFF][j] = DoS0/(1+gmx::square(DoS0*M_PI*nu[j]/(6*f*Natom)));
dos[DOS_SOLID][j] = dos[DOS][j]-dos[DOS_DIFF][j];
fprintf(fp, "%10g %10g %10g %10g\n",
recip_fac*nu[j],
dos[DOS][j]/recip_fac,
dos[DOS_SOLID][j]/recip_fac,
dos[DOS_DIFF][j]/recip_fac);
}
xvgrclose(fp);
/* Finally analyze the results! */
wCdiff = 0.5;
wSdiff = Shs/(3*BOLTZ); /* Is this correct? */
wEdiff = 0.5;
wAdiff = wEdiff-wSdiff;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_CP][j] = (dos[DOS_DIFF][j]*wCdiff +
dos[DOS_SOLID][j]*wCsolid(nu[j], beta));
dos[DOS_S][j] = (dos[DOS_DIFF][j]*wSdiff +
dos[DOS_SOLID][j]*wSsolid(nu[j], beta));
dos[DOS_A][j] = (dos[DOS_DIFF][j]*wAdiff +
dos[DOS_SOLID][j]*wAsolid(nu[j], beta));
dos[DOS_E][j] = (dos[DOS_DIFF][j]*wEdiff +
dos[DOS_SOLID][j]*wEsolid(nu[j], beta));
}
DiffCoeff = evaluate_integral(nframes/2, tt, dos[VACF], NULL, nframes/2, &stddev);
DiffCoeff = 1000*DiffCoeff/3.0;
fprintf(fplog, "Diffusion coefficient from VACF %g 10^-5 cm^2/s\n",
DiffCoeff);
fprintf(fplog, "Diffusion coefficient from DoS %g 10^-5 cm^2/s\n",
1000*DoS0/(12*tmass*beta));
cP = BOLTZ * evaluate_integral(nframes/4, nu, dos[DOS_CP], NULL,
nframes/4, &stddev);
fprintf(fplog, "Heat capacity %g J/mol K\n", 1000*cP/Nmol);
fprintf(fplog, "\nArrivederci!\n");
gmx_fio_fclose(fplog);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
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_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;
}
static void estimate_error(char *eefile,int nb_min,int resol,int n,int nset,
double *av,double *sig,real **val,real dt,
bool bFitAc,bool bSingleExpFit,bool bAllowNegLTCorr)
{
FILE *fp;
int bs,prev_bs,nbs,nb;
real spacing,nbr;
int s,i,j;
double blav,var;
char **leg;
real *tbs,*ybs,rtmp,dens,*fitsig,twooe,tau1_est,tau_sig;
real fitparm[4];
real ee,a,tau1,tau2;
if (n < 4)
{
fprintf(stdout,"The number of points is smaller than 4, can not make an error estimate\n");
return;
}
fp = xvgropen(eefile,"Error estimates",
"Block size (time)","Error estimate");
if (bPrintXvgrCodes())
{
fprintf(fp,
"@ subtitle \"using block averaging, total time %g (%d points)\"\n",
(n-1)*dt,n);
}
snew(leg,2*nset);
xvgr_legend(fp,2*nset,leg);
sfree(leg);
spacing = pow(2,1.0/resol);
snew(tbs,n);
snew(ybs,n);
snew(fitsig,n);
for(s=0; s<nset; s++)
{
nbs = 0;
prev_bs = 0;
nbr = nb_min;
while (nbr <= n)
{
bs = n/(int)nbr;
if (bs != prev_bs)
{
nb = n/bs;
var = 0;
for(i=0; i<nb; i++)
{
blav=0;
for (j=0; j<bs; j++)
{
blav += val[s][bs*i+j];
}
var += sqr(av[s] - blav/bs);
}
tbs[nbs] = bs*dt;
if (sig[s] == 0)
{
ybs[nbs] = 0;
}
else
{
ybs[nbs] = var/(nb*(nb-1.0))*(n*dt)/(sig[s]*sig[s]);
}
nbs++;
}
nbr *= spacing;
nb = (int)(nbr+0.5);
prev_bs = bs;
}
if (sig[s] == 0)
{
ee = 0;
a = 1;
tau1 = 0;
tau2 = 0;
}
else
{
for(i=0; i<nbs/2; i++)
{
rtmp = tbs[i];
tbs[i] = tbs[nbs-1-i];
tbs[nbs-1-i] = rtmp;
rtmp = ybs[i];
ybs[i] = ybs[nbs-1-i];
ybs[nbs-1-i] = rtmp;
}
/* The initial slope of the normalized ybs^2 is 1.
* For a single exponential autocorrelation: ybs(tau1) = 2/e tau1
* From this we take our initial guess for tau1.
*/
twooe = 2/exp(1);
i = -1;
do
{
i++;
tau1_est = tbs[i];
} while (i < nbs - 1 &&
(ybs[i] > ybs[i+1] || ybs[i] > twooe*tau1_est));
if (ybs[0] > ybs[1])
{
fprintf(stdout,"Data set %d has strange time correlations:\n"
"the std. error using single points is larger than that of blocks of 2 points\n"
"The error estimate might be inaccurate, check the fit\n",
s+1);
/* Use the total time as tau for the fitting weights */
tau_sig = (n - 1)*dt;
}
else
{
tau_sig = tau1_est;
}
if (debug)
{
fprintf(debug,"set %d tau1 estimate %f\n",s+1,tau1_est);
}
/* Generate more or less appropriate sigma's,
* also taking the density of points into account.
*/
for(i=0; i<nbs; i++)
{
if (i == 0)
{
dens = tbs[1]/tbs[0] - 1;
}
else if (i == nbs-1)
{
dens = tbs[nbs-1]/tbs[nbs-2] - 1;
}
else
{
dens = 0.5*(tbs[i+1]/tbs[i-1] - 1);
}
fitsig[i] = sqrt((tau_sig + tbs[i])/dens);
}
if (!bSingleExpFit)
{
fitparm[0] = tau1_est;
fitparm[1] = 0.95;
/* We set the initial guess for tau2
* to halfway between tau1_est and the total time (on log scale).
*/
fitparm[2] = sqrt(tau1_est*(n-1)*dt);
do_lmfit(nbs,ybs,fitsig,0,tbs,0,dt*n,bDebugMode(),effnERREST,fitparm,0);
fitparm[3] = 1-fitparm[1];
}
if (bSingleExpFit || fitparm[0]<0 || fitparm[2]<0 || fitparm[1]<0
|| (fitparm[1]>1 && !bAllowNegLTCorr) || fitparm[2]>(n-1)*dt)
{
if (!bSingleExpFit)
{
if (fitparm[2] > (n-1)*dt)
{
fprintf(stdout,
"Warning: tau2 is longer than the length of the data (%g)\n"
" the statistics might be bad\n",
(n-1)*dt);
}
else
{
fprintf(stdout,"a fitted parameter is negative\n");
}
fprintf(stdout,"invalid fit: e.e. %g a %g tau1 %g tau2 %g\n",
sig[s]*anal_ee_inf(fitparm,n*dt),
fitparm[1],fitparm[0],fitparm[2]);
/* Do a fit with tau2 fixed at the total time.
* One could also choose any other large value for tau2.
*/
fitparm[0] = tau1_est;
fitparm[1] = 0.95;
fitparm[2] = (n-1)*dt;
fprintf(stderr,"Will fix tau2 at the total time: %g\n",fitparm[2]);
do_lmfit(nbs,ybs,fitsig,0,tbs,0,dt*n,bDebugMode(),effnERREST,fitparm,4);
fitparm[3] = 1-fitparm[1];
}
if (bSingleExpFit || fitparm[0]<0 || fitparm[1]<0
|| (fitparm[1]>1 && !bAllowNegLTCorr))
{
if (!bSingleExpFit) {
fprintf(stdout,"a fitted parameter is negative\n");
fprintf(stdout,"invalid fit: e.e. %g a %g tau1 %g tau2 %g\n",
sig[s]*anal_ee_inf(fitparm,n*dt),
fitparm[1],fitparm[0],fitparm[2]);
}
/* Do a single exponential fit */
fprintf(stderr,"Will use a single exponential fit for set %d\n",s+1);
fitparm[0] = tau1_est;
fitparm[1] = 1.0;
fitparm[2] = 0.0;
do_lmfit(nbs,ybs,fitsig,0,tbs,0,dt*n,bDebugMode(),effnERREST,fitparm,6);
fitparm[3] = 1-fitparm[1];
}
}
ee = sig[s]*anal_ee_inf(fitparm,n*dt);
a = fitparm[1];
tau1 = fitparm[0];
tau2 = fitparm[2];
}
fprintf(stdout,"Set %3d: err.est. %g a %g tau1 %g tau2 %g\n",
s+1,ee,a,tau1,tau2);
fprintf(fp,"@ legend string %d \"av %f\"\n",2*s,av[s]);
fprintf(fp,"@ legend string %d \"ee %6g\"\n",
2*s+1,sig[s]*anal_ee_inf(fitparm,n*dt));
for(i=0; i<nbs; i++)
{
fprintf(fp,"%g %g %g\n",tbs[i],sig[s]*sqrt(ybs[i]/(n*dt)),
sig[s]*sqrt(fit_function(effnERREST,fitparm,tbs[i])/(n*dt)));
}
if (bFitAc)
{
int fitlen;
real *ac,acint,ac_fit[4];
snew(ac,n);
for(i=0; i<n; i++) {
ac[i] = val[s][i] - av[s];
if (i > 0)
fitsig[i] = sqrt(i);
else
fitsig[i] = 1;
}
low_do_autocorr(NULL,NULL,n,1,-1,&ac,
dt,eacNormal,1,FALSE,TRUE,
FALSE,0,0,effnNONE,0);
fitlen = n/nb_min;
/* Integrate ACF only up to fitlen/2 to avoid integrating noise */
acint = 0.5*ac[0];
for(i=1; i<=fitlen/2; i++)
{
acint += ac[i];
}
acint *= dt;
/* Generate more or less appropriate sigma's */
for(i=0; i<=fitlen; i++)
{
fitsig[i] = sqrt(acint + dt*i);
}
ac_fit[0] = 0.5*acint;
ac_fit[1] = 0.95;
ac_fit[2] = 10*acint;
do_lmfit(n/nb_min,ac,fitsig,dt,0,0,fitlen*dt,
bDebugMode(),effnEXP3,ac_fit,0);
ac_fit[3] = 1 - ac_fit[1];
fprintf(stdout,"Set %3d: ac erest %g a %g tau1 %g tau2 %g\n",
s+1,sig[s]*anal_ee_inf(ac_fit,n*dt),
ac_fit[1],ac_fit[0],ac_fit[2]);
fprintf(fp,"&\n");
for(i=0; i<nbs; i++)
{
fprintf(fp,"%g %g\n",tbs[i],
sig[s]*sqrt(fit_function(effnERREST,ac_fit,tbs[i]))/(n*dt));
}
sfree(ac);
}
if (s < nset-1)
{
fprintf(fp,"&\n");
}
}
sfree(fitsig);
sfree(ybs);
sfree(tbs);
fclose(fp);
}
int
gmx_select(int argc, char *argv[])
{
const char *desc[] = {
"g_select writes out basic data about dynamic selections.",
"It can be used for some simple analyses, or the output can",
"be combined with output from other programs and/or external",
"analysis programs to calculate more complex things.",
"Any combination of the output options is possible, but note",
"that [TT]-om[tt] only operates on the first selection.[PAR]",
"With [TT]-os[tt], calculates the number of positions in each",
"selection for each frame. With [TT]-norm[tt], the output is",
"between 0 and 1 and describes the fraction from the maximum",
"number of positions (e.g., for selection 'resname RA and x < 5'",
"the maximum number of positions is the number of atoms in",
"RA residues). With [TT]-cfnorm[tt], the output is divided",
"by the fraction covered by the selection.",
"[TT]-norm[tt] and [TT]-cfnorm[tt] can be specified independently",
"of one another.[PAR]",
"With [TT]-oc[tt], the fraction covered by each selection is",
"written out as a function of time.[PAR]",
"With [TT]-oi[tt], the selected atoms/residues/molecules are",
"written out as a function of time. In the output, the first",
"column contains the frame time, the second contains the number",
"of positions, followed by the atom/residue/molecule numbers.",
"If more than one selection is specified, the size of the second",
"group immediately follows the last number of the first group",
"and so on. With [TT]-dump[tt], the frame time and the number",
"of positions is omitted from the output. In this case, only one",
"selection can be given.[PAR]",
"With [TT]-om[tt], a mask is printed for the first selection",
"as a function of time. Each line in the output corresponds to",
"one frame, and contains either 0/1 for each atom/residue/molecule",
"possibly selected. 1 stands for the atom/residue/molecule being",
"selected for the current frame, 0 for not selected.",
"With [TT]-dump[tt], the frame time is omitted from the output.",
};
bool bDump = FALSE;
bool bFracNorm = FALSE;
bool bTotNorm = FALSE;
t_pargs pa[] = {
{"-dump", FALSE, etBOOL, {&bDump},
"Do not print the frame time (-om, -oi) or the index size (-oi)"},
{"-norm", FALSE, etBOOL, {&bTotNorm},
"Normalize by total number of positions with -os"},
{"-cfnorm", FALSE, etBOOL, {&bFracNorm},
"Normalize by covered fraction with -os"},
};
t_filenm fnm[] = {
{efXVG, "-os", "size.xvg", ffOPTWR},
{efXVG, "-oc", "cfrac.xvg", ffOPTWR},
{efDAT, "-oi", "index.dat", ffOPTWR},
{efDAT, "-om", "mask.dat", ffOPTWR},
};
#define NFILE asize(fnm)
gmx_ana_traj_t *trj;
t_topology *top;
int ngrps;
gmx_ana_selection_t **sel;
char **grpnames;
t_dsdata d;
char *fnSize, *fnFrac, *fnIndex, *fnMask;
int g;
int rc;
CopyRight(stderr, argv[0]);
gmx_ana_traj_create(&trj, 0);
gmx_ana_set_nanagrps(trj, -1);
parse_trjana_args(trj, &argc, argv, 0,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL);
gmx_ana_get_nanagrps(trj, &ngrps);
gmx_ana_get_anagrps(trj, &sel);
gmx_ana_init_coverfrac(trj, CFRAC_SOLIDANGLE);
/* Get output file names */
fnSize = opt2fn_null("-os", NFILE, fnm);
fnFrac = opt2fn_null("-oc", NFILE, fnm);
fnIndex = opt2fn_null("-oi", NFILE, fnm);
fnMask = opt2fn_null("-om", NFILE, fnm);
/* Write out sizes if nothing specified */
if (!fnFrac && !fnIndex && !fnMask)
{
fnSize = opt2fn("-os", NFILE, fnm);
}
if (bDump && ngrps > 1)
{
gmx_fatal(FARGS, "Only one index group allowed with -dump");
}
if (fnMask && ngrps > 1)
{
fprintf(stderr, "warning: the mask (-om) will only be written for the first group\n");
}
if (fnMask && !sel[0]->bDynamic)
{
fprintf(stderr, "warning: will not write the mask (-om) for a static selection\n");
fnMask = NULL;
}
/* Initialize reference calculation for masks */
if (fnMask)
{
gmx_ana_get_topology(trj, FALSE, &top, NULL);
snew(d.mmap, 1);
gmx_ana_indexmap_init(d.mmap, sel[0]->g, top, sel[0]->p.m.type);
}
/* Initialize calculation data */
d.bDump = bDump;
d.bFracNorm = bFracNorm;
snew(d.size, ngrps);
for (g = 0; g < ngrps; ++g)
{
d.size[g] = bTotNorm ? sel[g]->p.nr : 1;
}
/* Open output files */
d.sfp = d.cfp = d.ifp = d.mfp = NULL;
gmx_ana_get_grpnames(trj, &grpnames);
if (fnSize)
{
d.sfp = xvgropen(fnSize, "Selection size", "Time (ps)", "Number");
xvgr_selections(d.sfp, trj);
xvgr_legend(d.sfp, ngrps, grpnames);
}
if (fnFrac)
{
d.cfp = xvgropen(fnFrac, "Covered fraction", "Time (ps)", "Fraction");
xvgr_selections(d.cfp, trj);
xvgr_legend(d.cfp, ngrps, grpnames);
}
if (fnIndex)
{
d.ifp = ffopen(fnIndex, "w");
xvgr_selections(d.ifp, trj);
}
if (fnMask)
{
d.mfp = ffopen(fnMask, "w");
xvgr_selections(d.mfp, trj);
}
/* Do the analysis and write out results */
gmx_ana_do(trj, 0, &print_data, &d);
/* Close the files */
if (d.sfp)
{
fclose(d.sfp);
}
if (d.cfp)
{
fclose(d.cfp);
}
if (d.ifp)
{
fclose(d.ifp);
}
if (d.mfp)
{
fclose(d.mfp);
}
thanx(stderr);
return 0;
}
int gmx_dos(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_dos[tt] computes the Density of States from a simulations.",
"In order for this to be meaningful the velocities must be saved",
"in the trajecotry with sufficiently high frequency such as to cover",
"all vibrations. For flexible systems that would be around a few fs",
"between saving. Properties based on the DoS are printed on the",
"standard output."
};
const char *bugs[] = {
"This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision)."
};
FILE *fp, *fplog;
t_topology top;
int ePBC = -1;
t_trxframe fr;
matrix box;
int gnx;
char title[256];
real t0, t1, m;
t_trxstatus *status;
int nV, nframes, n_alloc, i, j, k, l, fftcode, Nmol, Natom;
double rho, dt, V2sum, Vsum, V, tmass, dostot, dos2, dosabs;
real **c1, **dos, mi, beta, bfac, *nu, *tt, stddev, c1j;
output_env_t oenv;
gmx_fft_t fft;
double cP, S, A, E, DiffCoeff, Delta, f, y, z, sigHS, Shs, Sig, DoS0, recip_fac;
double wCdiff, wSdiff, wAdiff, wEdiff;
static gmx_bool bVerbose = TRUE, bAbsolute = FALSE, bNormalize = FALSE;
static gmx_bool bRecip = FALSE, bDump = FALSE;
static real Temp = 298.15, toler = 1e-6;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy." },
{ "-recip", FALSE, etBOOL, {&bRecip},
"Use cm^-1 on X-axis instead of 1/ps for DoS plots." },
{ "-abs", FALSE, etBOOL, {&bAbsolute},
"Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only" },
{ "-normdos", FALSE, etBOOL, {&bNormalize},
"Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary." },
{ "-T", FALSE, etREAL, {&Temp},
"Temperature in the simulation" },
{ "-toler", FALSE, etREAL, {&toler},
"[HIDDEN]Tolerance when computing the fluidicity using bisection algorithm" },
{ "-dump", FALSE, etBOOL, {&bDump},
"[HIDDEN]Dump the y/fy plot corresponding to Fig. 2 inLin2003a and the and the weighting functions corresponding to Fig. 1 in Berens1983a." }
};
t_filenm fnm[] = {
{ efTRN, "-f", NULL, ffREAD },
{ efTPX, "-s", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-vacf", "vacf", ffWRITE },
{ efXVG, "-mvacf", "mvacf", ffWRITE },
{ efXVG, "-dos", "dos", ffWRITE },
{ efLOG, "-g", "dos", ffWRITE },
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
const char *DoSlegend[] = {
"DoS(v)", "DoS(v)[Solid]", "DoS(v)[Diff]"
};
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);
beta = 1/(Temp*BOLTZ);
if (bDump)
{
printf("Dumping reference figures. Thanks for your patience.\n");
dump_fy(oenv, toler);
dump_w(oenv, beta);
exit(0);
}
fplog = gmx_fio_fopen(ftp2fn(efLOG, NFILE, fnm), "w");
fprintf(fplog, "Doing density of states analysis based on trajectory.\n");
please_cite(fplog, "Pascal2011a");
please_cite(fplog, "Caleman2011b");
read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
TRUE);
V = det(box);
tmass = 0;
for (i = 0; (i < top.atoms.nr); i++)
{
tmass += top.atoms.atom[i].m;
}
Natom = top.atoms.nr;
Nmol = top.mols.nr;
gnx = Natom*DIM;
/* 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;
nframes = 0;
Vsum = V2sum = 0;
nV = 0;
do
{
if (fr.bBox)
{
V = det(fr.box);
V2sum += V*V;
Vsum += V;
nV++;
}
if (nframes >= n_alloc)
{
n_alloc += 100;
for (i = 0; i < gnx; i++)
{
srenew(c1[i], n_alloc);
}
}
for (i = 0; i < gnx; i += DIM)
{
c1[i+XX][nframes] = fr.v[i/DIM][XX];
c1[i+YY][nframes] = fr.v[i/DIM][YY];
c1[i+ZZ][nframes] = fr.v[i/DIM][ZZ];
}
t1 = fr.time;
nframes++;
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
dt = (t1-t0)/(nframes-1);
if (nV > 0)
{
V = Vsum/nV;
}
if (bVerbose)
{
printf("Going to do %d fourier transforms of length %d. Hang on.\n",
gnx, nframes);
}
low_do_autocorr(NULL, oenv, NULL, nframes, gnx, nframes, c1, dt, eacNormal, 0, FALSE,
FALSE, FALSE, -1, -1, 0, 0);
snew(dos, DOS_NR);
for (j = 0; (j < DOS_NR); j++)
{
snew(dos[j], nframes+4);
}
if (bVerbose)
{
printf("Going to merge the ACFs into the mass-weighted and plain ACF\n");
}
for (i = 0; (i < gnx); i += DIM)
{
mi = top.atoms.atom[i/DIM].m;
for (j = 0; (j < nframes/2); j++)
{
c1j = (c1[i+XX][j] + c1[i+YY][j] + c1[i+ZZ][j]);
dos[VACF][j] += c1j/Natom;
dos[MVACF][j] += mi*c1j;
}
}
fp = xvgropen(opt2fn("-vacf", NFILE, fnm), "Velocity ACF",
"Time (ps)", "C(t)", oenv);
snew(tt, nframes/2);
for (j = 0; (j < nframes/2); j++)
{
tt[j] = j*dt;
fprintf(fp, "%10g %10g\n", tt[j], dos[VACF][j]);
}
xvgrclose(fp);
fp = xvgropen(opt2fn("-mvacf", NFILE, fnm), "Mass-weighted velocity ACF",
"Time (ps)", "C(t)", oenv);
for (j = 0; (j < nframes/2); j++)
{
fprintf(fp, "%10g %10g\n", tt[j], dos[MVACF][j]);
}
xvgrclose(fp);
if ((fftcode = gmx_fft_init_1d_real(&fft, nframes/2,
GMX_FFT_FLAG_NONE)) != 0)
{
gmx_fatal(FARGS, "gmx_fft_init_1d_real returned %d", fftcode);
}
if ((fftcode = gmx_fft_1d_real(fft, GMX_FFT_REAL_TO_COMPLEX,
(void *)dos[MVACF], (void *)dos[DOS])) != 0)
{
gmx_fatal(FARGS, "gmx_fft_1d_real returned %d", fftcode);
}
/* First compute the DoS */
/* Magic factor of 8 included now. */
bfac = 8*dt*beta/2;
dos2 = 0;
snew(nu, nframes/4);
for (j = 0; (j < nframes/4); j++)
{
nu[j] = 2*j/(t1-t0);
dos2 += sqr(dos[DOS][2*j]) + sqr(dos[DOS][2*j+1]);
if (bAbsolute)
{
dos[DOS][j] = bfac*sqrt(sqr(dos[DOS][2*j]) + sqr(dos[DOS][2*j+1]));
}
else
{
dos[DOS][j] = bfac*dos[DOS][2*j];
}
}
/* Normalize it */
dostot = evaluate_integral(nframes/4, nu, dos[DOS], NULL, nframes/4, &stddev);
if (bNormalize)
{
for (j = 0; (j < nframes/4); j++)
{
dos[DOS][j] *= 3*Natom/dostot;
}
}
/* Now analyze it */
DoS0 = dos[DOS][0];
/* Note this eqn. is incorrect in Pascal2011a! */
Delta = ((2*DoS0/(9*Natom))*sqrt(M_PI*BOLTZ*Temp*Natom/tmass)*
pow((Natom/V), 1.0/3.0)*pow(6/M_PI, 2.0/3.0));
f = calc_fluidicity(Delta, toler);
y = calc_y(f, Delta, toler);
z = calc_compress(y);
Sig = BOLTZ*(5.0/2.0+log(2*M_PI*BOLTZ*Temp/(sqr(PLANCK))*V/(f*Natom)));
Shs = Sig+calc_Shs(f, y);
rho = (tmass*AMU)/(V*NANO*NANO*NANO);
sigHS = pow(6*y*V/(M_PI*Natom), 1.0/3.0);
fprintf(fplog, "System = \"%s\"\n", title);
fprintf(fplog, "Nmol = %d\n", Nmol);
fprintf(fplog, "Natom = %d\n", Natom);
fprintf(fplog, "dt = %g ps\n", dt);
fprintf(fplog, "tmass = %g amu\n", tmass);
fprintf(fplog, "V = %g nm^3\n", V);
fprintf(fplog, "rho = %g g/l\n", rho);
fprintf(fplog, "T = %g K\n", Temp);
fprintf(fplog, "beta = %g mol/kJ\n", beta);
fprintf(fplog, "\nDoS parameters\n");
fprintf(fplog, "Delta = %g\n", Delta);
fprintf(fplog, "fluidicity = %g\n", f);
fprintf(fplog, "hard sphere packing fraction = %g\n", y);
fprintf(fplog, "hard sphere compressibility = %g\n", z);
fprintf(fplog, "ideal gas entropy = %g\n", Sig);
fprintf(fplog, "hard sphere entropy = %g\n", Shs);
fprintf(fplog, "sigma_HS = %g nm\n", sigHS);
fprintf(fplog, "DoS0 = %g\n", DoS0);
fprintf(fplog, "Dos2 = %g\n", dos2);
fprintf(fplog, "DoSTot = %g\n", dostot);
/* Now compute solid (2) and diffusive (3) components */
fp = xvgropen(opt2fn("-dos", NFILE, fnm), "Density of states",
bRecip ? "E (cm\\S-1\\N)" : "\\f{12}n\\f{4} (1/ps)",
"\\f{4}S(\\f{12}n\\f{4})", oenv);
xvgr_legend(fp, asize(DoSlegend), DoSlegend, oenv);
recip_fac = bRecip ? (1e7/SPEED_OF_LIGHT) : 1.0;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_DIFF][j] = DoS0/(1+sqr(DoS0*M_PI*nu[j]/(6*f*Natom)));
dos[DOS_SOLID][j] = dos[DOS][j]-dos[DOS_DIFF][j];
fprintf(fp, "%10g %10g %10g %10g\n",
recip_fac*nu[j],
dos[DOS][j]/recip_fac,
dos[DOS_SOLID][j]/recip_fac,
dos[DOS_DIFF][j]/recip_fac);
}
xvgrclose(fp);
/* Finally analyze the results! */
wCdiff = 0.5;
wSdiff = Shs/(3*BOLTZ); /* Is this correct? */
wEdiff = 0.5;
wAdiff = wEdiff-wSdiff;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_CP][j] = (dos[DOS_DIFF][j]*wCdiff +
dos[DOS_SOLID][j]*wCsolid(nu[j], beta));
dos[DOS_S][j] = (dos[DOS_DIFF][j]*wSdiff +
dos[DOS_SOLID][j]*wSsolid(nu[j], beta));
dos[DOS_A][j] = (dos[DOS_DIFF][j]*wAdiff +
dos[DOS_SOLID][j]*wAsolid(nu[j], beta));
dos[DOS_E][j] = (dos[DOS_DIFF][j]*wEdiff +
dos[DOS_SOLID][j]*wEsolid(nu[j], beta));
}
DiffCoeff = evaluate_integral(nframes/2, tt, dos[VACF], NULL, nframes/2, &stddev);
DiffCoeff = 1000*DiffCoeff/3.0;
fprintf(fplog, "Diffusion coefficient from VACF %g 10^-5 cm^2/s\n",
DiffCoeff);
fprintf(fplog, "Diffusion coefficient from DoS %g 10^-5 cm^2/s\n",
1000*DoS0/(12*tmass*beta));
cP = BOLTZ * evaluate_integral(nframes/4, nu, dos[DOS_CP], NULL,
nframes/4, &stddev);
fprintf(fplog, "Heat capacity %g J/mol K\n", 1000*cP/Nmol);
/*
S = BOLTZ * evaluate_integral(nframes/4,nu,dos[DOS_S],NULL,
nframes/4,&stddev);
fprintf(fplog,"Entropy %g J/mol K\n",1000*S/Nmol);
A = BOLTZ * evaluate_integral(nframes/4,nu,dos[DOS_A],NULL,
nframes/4,&stddev);
fprintf(fplog,"Helmholtz energy %g kJ/mol\n",A/Nmol);
E = BOLTZ * evaluate_integral(nframes/4,nu,dos[DOS_E],NULL,
nframes/4,&stddev);
fprintf(fplog,"Internal energy %g kJ/mol\n",E/Nmol);
*/
fprintf(fplog, "\nArrivederci!\n");
gmx_fio_fclose(fplog);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
thanx(stderr);
return 0;
}
static void pr_ff(t_coupl_rec *tcr,real time,t_idef *idef,
t_commrec *cr,int nfile,t_filenm fnm[])
{
static FILE *prop;
static FILE **out=NULL;
static FILE **qq=NULL;
static FILE **ip=NULL;
t_coupl_LJ *tclj;
t_coupl_BU *tcbu;
char buf[256];
char *leg[] = { "C12", "C6" };
char *eleg[] = { "Epsilon", "Sigma" };
char *bleg[] = { "A", "B", "C" };
char **raleg;
int i,j,index;
if ((prop == NULL) && (out == NULL) && (qq == NULL) && (ip == NULL)) {
prop=xvgropen(opt2fn("-runav",nfile,fnm),
"Properties and Running Averages","Time (ps)","");
snew(raleg,2*eoObsNR);
for(i=j=0; (i<eoObsNR); i++) {
if (tcr->bObsUsed[i]) {
raleg[j++] = strdup(eoNames[i]);
sprintf(buf,"RA-%s",eoNames[i]);
raleg[j++] = strdup(buf);
}
}
xvgr_legend(prop,j,raleg);
for(i=0; (i<j); i++)
sfree(raleg[i]);
sfree(raleg);
if (tcr->nLJ) {
snew(out,tcr->nLJ);
for(i=0; (i<tcr->nLJ); i++) {
if (tcr->tcLJ[i].bPrint) {
tclj = &(tcr->tcLJ[i]);
out[i] =
xvgropen(mk_gct_nm(opt2fn("-ffout",nfile,fnm),
efXVG,tclj->at_i,tclj->at_j),
"General Coupling Lennard Jones","Time (ps)",
"Force constant (units)");
fprintf(out[i],"@ subtitle \"Interaction between types %d and %d\"\n",
tclj->at_i,tclj->at_j);
if (tcr->combrule == 1)
xvgr_legend(out[i],asize(leg),leg);
else
xvgr_legend(out[i],asize(eleg),eleg);
fflush(out[i]);
}
}
}
else if (tcr->nBU) {
snew(out,tcr->nBU);
for(i=0; (i<tcr->nBU); i++) {
if (tcr->tcBU[i].bPrint) {
tcbu=&(tcr->tcBU[i]);
out[i] =
xvgropen(mk_gct_nm(opt2fn("-ffout",nfile,fnm),efXVG,
tcbu->at_i,tcbu->at_j),
"General Coupling Buckingham","Time (ps)",
"Force constant (units)");
fprintf(out[i],"@ subtitle \"Interaction between types %d and %d\"\n",
tcbu->at_i,tcbu->at_j);
xvgr_legend(out[i],asize(bleg),bleg);
fflush(out[i]);
}
}
}
snew(qq,tcr->nQ);
for(i=0; (i<tcr->nQ); i++) {
if (tcr->tcQ[i].bPrint) {
qq[i] = xvgropen(mk_gct_nm(opt2fn("-ffout",nfile,fnm),efXVG,
tcr->tcQ[i].at_i,-1),
"General Coupling Charge","Time (ps)","Charge (e)");
fprintf(qq[i],"@ subtitle \"Type %d\"\n",tcr->tcQ[i].at_i);
fflush(qq[i]);
}
}
snew(ip,tcr->nIP);
for(i=0; (i<tcr->nIP); i++) {
sprintf(buf,"gctIP%d",tcr->tIP[i].type);
ip[i]=xvgropen(mk_gct_nm(opt2fn("-ffout",nfile,fnm),efXVG,0,-1),
"General Coupling iparams","Time (ps)","ip ()");
index=tcr->tIP[i].type;
fprintf(ip[i],"@ subtitle \"Coupling to %s\"\n",
interaction_function[idef->functype[index]].longname);
fflush(ip[i]);
}
}
/* Write properties to file */
fprintf(prop,"%10.3f",time);
for(i=0; (i<eoObsNR); i++)
if (tcr->bObsUsed[i])
fprintf(prop," %10.3e %10.3e",tcr->act_value[i],tcr->av_value[i]);
fprintf(prop,"\n");
fflush(prop);
for(i=0; (i<tcr->nLJ); i++) {
tclj=&(tcr->tcLJ[i]);
if (tclj->bPrint) {
if (tcr->combrule == 1)
fprintf(out[i],"%14.7e %14.7e %14.7e\n",
time,tclj->c12,tclj->c6);
else {
double sigma = pow(tclj->c12/tclj->c6,1.0/6.0);
double epsilon = 0.25*sqr(tclj->c6)/tclj->c12;
fprintf(out[i],"%14.7e %14.7e %14.7e\n",
time,epsilon,sigma);
}
fflush(out[i]);
}
}
for(i=0; (i<tcr->nBU); i++) {
tcbu=&(tcr->tcBU[i]);
if (tcbu->bPrint) {
fprintf(out[i],"%14.7e %14.7e %14.7e %14.7e\n",
time,tcbu->a,tcbu->b,tcbu->c);
fflush(out[i]);
}
}
for(i=0; (i<tcr->nQ); i++) {
if (tcr->tcQ[i].bPrint) {
fprintf(qq[i],"%14.7e %14.7e\n",time,tcr->tcQ[i].Q);
fflush(qq[i]);
}
}
for(i=0; (i<tcr->nIP); i++) {
fprintf(ip[i],"%10g ",time);
index=tcr->tIP[i].type;
switch(idef->functype[index]) {
case F_BONDS:
fprintf(ip[i],"%10g %10g\n",tcr->tIP[i].iprint.harmonic.krA,
tcr->tIP[i].iprint.harmonic.rA);
break;
default:
break;
}
fflush(ip[i]);
}
}
int gmx_saltbr(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_saltbr[tt] plots the distance between all combination of charged groups",
"as a function of time. The groups are combined in different ways.",
"A minimum distance can be given (i.e. a cut-off), such that groups",
"that are never closer than that distance will not be plotted.[PAR]",
"Output will be in a number of fixed filenames, [TT]min-min.xvg[tt], [TT]plus-min.xvg[tt]",
"and [TT]plus-plus.xvg[tt], or files for every individual ion pair if the [TT]-sep[tt]",
"option is selected. In this case, files are named as [TT]sb-(Resname)(Resnr)-(Atomnr)[tt].",
"There may be [BB]many[bb] such files."
};
static gmx_bool bSep = FALSE;
static real truncate = 1000.0;
t_pargs pa[] = {
{ "-t", FALSE, etREAL, {&truncate},
"Groups that are never closer than this distance are not plotted" },
{ "-sep", FALSE, etBOOL, {&bSep},
"Use separate files for each interaction (may be MANY)" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPX, NULL, NULL, ffREAD },
};
#define NFILE asize(fnm)
FILE *out[3], *fp;
static const char *title[3] = {
"Distance between positively charged groups",
"Distance between negatively charged groups",
"Distance between oppositely charged groups"
};
static const char *fn[3] = {
"plus-plus.xvg",
"min-min.xvg",
"plus-min.xvg"
};
int nset[3] = {0, 0, 0};
t_topology *top;
int ePBC;
char *buf;
t_trxstatus *status;
int i, j, k, m, nnn, teller, ncg, n1, n2, n3, natoms;
real t, *time, qi, qj;
t_charge *cg;
real ***cgdist;
int **nWithin;
double t0, dt;
char label[234];
t_pbc pbc;
rvec *x;
matrix box;
output_env_t oenv;
parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
cg = mk_charge(&top->atoms, &(top->cgs), &ncg);
snew(cgdist, ncg);
snew(nWithin, ncg);
for (i = 0; (i < ncg); i++)
{
snew(cgdist[i], ncg);
snew(nWithin[i], ncg);
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
teller = 0;
time = NULL;
do
{
srenew(time, teller+1);
time[teller] = t;
set_pbc(&pbc, ePBC, box);
for (i = 0; (i < ncg); i++)
{
for (j = i+1; (j < ncg); j++)
{
srenew(cgdist[i][j], teller+1);
cgdist[i][j][teller] =
calc_dist(&pbc, x, &(top->cgs), cg[i].cg, cg[j].cg);
if (cgdist[i][j][teller] < truncate)
{
nWithin[i][j] = 1;
}
}
}
teller++;
}
while (read_next_x(oenv, status, &t, natoms, x, box));
fprintf(stderr, "\n");
close_trj(status);
if (bSep)
{
snew(buf, 256);
for (i = 0; (i < ncg); i++)
{
for (j = i+1; (j < ncg); j++)
{
if (nWithin[i][j])
{
sprintf(buf, "sb-%s:%s.xvg", cg[i].label, cg[j].label);
fp = xvgropen(buf, buf, "Time (ps)", "Distance (nm)", oenv);
for (k = 0; (k < teller); k++)
{
fprintf(fp, "%10g %10g\n", time[k], cgdist[i][j][k]);
}
ffclose(fp);
}
}
}
sfree(buf);
}
else
{
for (m = 0; (m < 3); m++)
{
out[m] = xvgropen(fn[m], title[m], "Time (ps)", "Distance (nm)", oenv);
}
snew(buf, 256);
for (i = 0; (i < ncg); i++)
{
qi = cg[i].q;
for (j = i+1; (j < ncg); j++)
{
qj = cg[j].q;
if (nWithin[i][j])
{
sprintf(buf, "%s:%s", cg[i].label, cg[j].label);
if (qi*qj < 0)
{
nnn = 2;
}
else if (qi+qj > 0)
{
nnn = 0;
}
else
{
nnn = 1;
}
if (nset[nnn] == 0)
{
xvgr_legend(out[nnn], 1, (const char**)&buf, oenv);
}
else
{
if (output_env_get_xvg_format(oenv) == exvgXMGR)
{
fprintf(out[nnn], "@ legend string %d \"%s\"\n", nset[nnn], buf);
}
else if (output_env_get_xvg_format(oenv) == exvgXMGRACE)
{
fprintf(out[nnn], "@ s%d legend \"%s\"\n", nset[nnn], buf);
}
}
nset[nnn]++;
nWithin[i][j] = nnn+1;
}
}
}
for (k = 0; (k < teller); k++)
{
for (m = 0; (m < 3); m++)
{
fprintf(out[m], "%10g", time[k]);
}
for (i = 0; (i < ncg); i++)
{
for (j = i+1; (j < ncg); j++)
{
nnn = nWithin[i][j];
if (nnn > 0)
{
fprintf(out[nnn-1], " %10g", cgdist[i][j][k]);
}
}
}
for (m = 0; (m < 3); m++)
{
fprintf(out[m], "\n");
}
}
for (m = 0; (m < 3); m++)
{
ffclose(out[m]);
if (nset[m] == 0)
{
remove(fn[m]);
}
}
}
thanx(stderr);
return 0;
}
int gmx_rotmat(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] plots the rotation matrix required for least squares fitting",
"a conformation onto the reference conformation provided with",
"[TT]-s[tt]. Translation is removed before fitting.",
"The output are the three vectors that give the new directions",
"of the x, y and z directions of the reference conformation,",
"for example: (zx,zy,zz) is the orientation of the reference",
"z-axis in the trajectory frame.",
"[PAR]",
"This tool is useful for, for instance,",
"determining the orientation of a molecule",
"at an interface, possibly on a trajectory produced with",
"[TT]gmx trjconv -fit rotxy+transxy[tt] to remove the rotation",
"in the [IT]x-y[it] plane.",
"[PAR]",
"Option [TT]-ref[tt] determines a reference structure for fitting,",
"instead of using the structure from [TT]-s[tt]. The structure with",
"the lowest sum of RMSD's to all other structures is used.",
"Since the computational cost of this procedure grows with",
"the square of the number of frames, the [TT]-skip[tt] option",
"can be useful. A full fit or only a fit in the [IT]x-y[it] plane can",
"be performed.",
"[PAR]",
"Option [TT]-fitxy[tt] fits in the [IT]x-y[it] plane before determining",
"the rotation matrix."
};
const char *reffit[] =
{ NULL, "none", "xyz", "xy", NULL };
static int skip = 1;
static gmx_bool bFitXY = FALSE, bMW = TRUE;
t_pargs pa[] = {
{ "-ref", FALSE, etENUM, {reffit},
"Determine the optimal reference structure" },
{ "-skip", FALSE, etINT, {&skip},
"Use every nr-th frame for [TT]-ref[tt]" },
{ "-fitxy", FALSE, etBOOL, {&bFitXY},
"Fit the x/y rotation before determining the rotation" },
{ "-mw", FALSE, etBOOL, {&bMW},
"Use mass weighted fitting" }
};
FILE *out;
t_trxstatus *status;
t_topology top;
int ePBC;
rvec *x_ref, *x;
matrix box, R;
real t;
int natoms, i;
char *grpname, title[256];
int gnx;
gmx_rmpbc_t gpbc = NULL;
atom_id *index;
output_env_t oenv;
real *w_rls;
const char *leg[] = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "rotmat", ffWRITE }
};
#define NFILE asize(fnm)
if (!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))
{
return 0;
}
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x_ref, NULL, box, bMW);
gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
gmx_rmpbc(gpbc, top.atoms.nr, box, x_ref);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
if (reffit[0][0] != 'n')
{
get_refx(oenv, ftp2fn(efTRX, NFILE, fnm), reffit[0][2] == 'z' ? 3 : 2, skip,
gnx, index, bMW, &top, ePBC, x_ref);
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(w_rls, natoms);
for (i = 0; i < gnx; i++)
{
if (index[i] >= natoms)
{
gmx_fatal(FARGS, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[i]+1, natoms);
}
w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
}
if (reffit[0][0] == 'n')
{
reset_x(gnx, index, natoms, NULL, x_ref, w_rls);
}
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Fit matrix", "Time (ps)", "", oenv);
xvgr_legend(out, NLEG, leg, oenv);
do
{
gmx_rmpbc(gpbc, natoms, box, x);
reset_x(gnx, index, natoms, NULL, x, w_rls);
if (bFitXY)
{
do_fit_ndim(2, natoms, w_rls, x_ref, x);
}
calc_fit_R(DIM, natoms, w_rls, x_ref, x, R);
fprintf(out,
"%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
t,
R[XX][XX], R[XX][YY], R[XX][ZZ],
R[YY][XX], R[YY][YY], R[YY][ZZ],
R[ZZ][XX], R[ZZ][YY], R[ZZ][ZZ]);
}
while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
close_trj(status);
gmx_ffclose(out);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
return 0;
}
int main(int argc,char *argv[])
{
static char *desc[] = {
"do_dssp ",
"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. do_dssp assumes that the dssp executable is",
"/usr/local/bin/dssp. If this is not the case, then you should",
"set an environment variable [BB]DSSP[bb] pointing to the dssp",
"executable, e.g.: [PAR]",
"[TT]setenv DSSP /opt/dssp/bin/dssp[tt][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].",
"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 [TT]g_sas[tt] 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 [TT]g_chi[tt]. Together",
"these two programs can be used to analyze dihedral properties as a",
"function of secondary structure type."
};
static bool bVerbose;
static char *ss_string="HEBT";
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"HIDDENGenerate miles of useless information" },
{ "-sss", FALSE, etSTR, {&ss_string},
"Secondary structures for structure count"}
};
int status;
FILE *tapein;
FILE *ss,*acc,*fTArea,*tmpf;
char *fnSCount,*fnArea,*fnTArea,*fnAArea;
char *leg[] = { "Phobic", "Phylic" };
t_topology top;
int ePBC;
t_atoms *atoms;
t_matrix mat;
int nres,nr0,naccr;
bool *bPhbres,bDoAccSurf;
real t;
int i,j,natoms,nframe=0;
matrix box;
int gnx;
char *grpnm,*ss_str;
atom_id *index;
rvec *xp,*x;
int *average_area;
real **accr,*av_area, *norm_av_area;
char pdbfile[32],tmpfile[32],title[256];
char dssp[256],*dptr;
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)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE ,
NFILE,fnm, asize(pa),pa, asize(desc),desc,0,NULL);
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]].resnr != nr0) {
nr0=atoms->atom[index[i]].resnr;
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 (!fexist(dptr))
gmx_fatal(FARGS,"DSSP executable (%s) does not exist (use setenv DSSP)",
dptr);
sprintf(dssp,"%s %s %s %s > /dev/null %s",
dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null");
if (bVerbose)
fprintf(stderr,"dssp cmd='%s'\n",dssp);
if (fnTArea) {
fTArea=xvgropen(fnTArea,"Solvent Accessible Surface Area",
xvgr_tlabel(),"Area (nm\\S2\\N)");
xvgr_legend(fTArea,2,leg);
} else
fTArea=NULL;
mat.map=NULL;
mat.nmap=getcmap(libopen(opt2fn("-map",NFILE,fnm)),
opt2fn("-map",NFILE,fnm),&(mat.map));
natoms=read_first_x(&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+10);
snew(av_area,atoms->nres+10);
snew(norm_av_area,atoms->nres+10);
accr=NULL;
naccr=0;
do {
t = convert_time(t);
if (nframe>=naccr) {
naccr+=10;
srenew(accr,naccr);
for(i=naccr-10; i<naccr; i++)
snew(accr[i],atoms->nres+10);
}
rm_pbc(&(top.idef),ePBC,natoms,box,x,x);
tapein=ffopen(pdbfile,"w");
write_pdbfile_indexed(tapein,NULL,atoms,x,ePBC,box,0,-1,gnx,index);
fclose(tapein);
#ifdef GMX_NO_SYSTEM
printf("Warning-- No calls to system(3) supported on this platform.");
printf("Warning-- Skipping execution of 'system(\"%s\")'.", dssp);
exit(1);
#else
if(0 != system(dssp))
{
gmx_fatal(FARGS,"Failed to execute command: %s",dssp);
}
#endif
strip_dssp(tmpfile,nres,bPhbres,t,
accr[nframe],fTArea,&mat,average_area);
remove(tmpfile);
remove(pdbfile);
nframe++;
} while(read_next_x(status,&t,natoms,x,box));
fprintf(stderr,"\n");
close_trj(status);
if (fTArea)
ffclose(fTArea);
prune_ss_legend(&mat);
ss=opt2FILE("-o",NFILE,fnm,"w");
write_xpm_m(ss,mat);
ffclose(ss);
if (opt2bSet("-ssdump",NFILE,fnm)) {
snew(ss_str,nres+1);
for(i=0; (i<nres); i++)
ss_str[i] = mat.map[mat.matrix[0][i]].code.c1;
ss_str[i] = '\0';
ss = opt2FILE("-ssdump",NFILE,fnm,"w");
fprintf(ss,"%d\n%s\n",nres,ss_str);
fclose(ss);
sfree(ss_str);
}
analyse_ss(fnSCount,&mat,ss_string);
if (bDoAccSurf) {
write_sas_mat(fnArea,accr,nframe,nres,&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");
for(i=0; (i<nres); i++)
fprintf(acc,"%5d %10g %10g\n",i+1,av_area[i], norm_av_area[i]);
ffclose(acc);
}
}
view_all(NFILE, fnm);
thanx(stderr);
return 0;
}
int gmx_enemat(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] extracts an energy matrix from the energy file ([TT]-f[tt]).",
"With [TT]-groups[tt] a file must be supplied with on each",
"line a group of atoms to be used. For these groups matrix of",
"interaction energies will be extracted from the energy file",
"by looking for energy groups with names corresponding to pairs",
"of groups of atoms, e.g. if your [TT]-groups[tt] file contains::",
"",
" 2",
" Protein",
" SOL",
"",
"then energy groups with names like 'Coul-SR:Protein-SOL' and ",
"'LJ:Protein-SOL' are expected in the energy file (although",
"[THISMODULE] is most useful if many groups are analyzed",
"simultaneously). Matrices for different energy types are written",
"out separately, as controlled by the",
"[TT]-[no]coul[tt], [TT]-[no]coulr[tt], [TT]-[no]coul14[tt], ",
"[TT]-[no]lj[tt], [TT]-[no]lj14[tt], ",
"[TT]-[no]bham[tt] and [TT]-[no]free[tt] options.",
"Finally, the total interaction energy energy per group can be ",
"calculated ([TT]-etot[tt]).[PAR]",
"An approximation of the free energy can be calculated using:",
"[MATH]E[SUB]free[sub] = E[SUB]0[sub] + kT [LOG][CHEVRON][EXP](E-E[SUB]0[sub])/kT[exp][chevron][log][math], where '[MATH][CHEVRON][chevron][math]'",
"stands for time-average. A file with reference free energies",
"can be supplied to calculate the free energy difference",
"with some reference state. Group names (e.g. residue names)",
"in the reference file should correspond to the group names",
"as used in the [TT]-groups[tt] file, but a appended number",
"(e.g. residue number) in the [TT]-groups[tt] will be ignored",
"in the comparison."
};
static gmx_bool bSum = FALSE;
static gmx_bool bMeanEmtx = TRUE;
static int skip = 0, nlevels = 20;
static real cutmax = 1e20, cutmin = -1e20, reftemp = 300.0;
static gmx_bool bCoulSR = TRUE, bCoul14 = FALSE;
static gmx_bool bLJSR = TRUE, bLJ14 = FALSE, bBhamSR = FALSE,
bFree = TRUE;
t_pargs pa[] = {
{ "-sum", FALSE, etBOOL, {&bSum},
"Sum the energy terms selected rather than display them all" },
{ "-skip", FALSE, etINT, {&skip},
"Skip number of frames between data points" },
{ "-mean", FALSE, etBOOL, {&bMeanEmtx},
"with [TT]-groups[tt] extracts matrix of mean energies instead of "
"matrix for each timestep" },
{ "-nlevels", FALSE, etINT, {&nlevels}, "number of levels for matrix colors"},
{ "-max", FALSE, etREAL, {&cutmax}, "max value for energies"},
{ "-min", FALSE, etREAL, {&cutmin}, "min value for energies"},
{ "-coulsr", FALSE, etBOOL, {&bCoulSR}, "extract Coulomb SR energies"},
{ "-coul14", FALSE, etBOOL, {&bCoul14}, "extract Coulomb 1-4 energies"},
{ "-ljsr", FALSE, etBOOL, {&bLJSR}, "extract Lennard-Jones SR energies"},
{ "-lj14", FALSE, etBOOL, {&bLJ14}, "extract Lennard-Jones 1-4 energies"},
{ "-bhamsr", FALSE, etBOOL, {&bBhamSR}, "extract Buckingham SR energies"},
{ "-free", FALSE, etBOOL, {&bFree}, "calculate free energy"},
{ "-temp", FALSE, etREAL, {&reftemp},
"reference temperature for free energy calculation"}
};
/* We will define egSP more energy-groups:
egTotal (total energy) */
#define egTotal egNR
#define egSP 1
gmx_bool egrp_use[egNR+egSP];
ener_file_t in;
FILE *out;
int timecheck = 0;
gmx_enxnm_t *enm = NULL;
t_enxframe *fr;
int teller = 0;
real sum;
gmx_bool bCont, bRef;
gmx_bool bCutmax, bCutmin;
real **eneset, *time = NULL;
int *set, i, j, k, prevk, m = 0, n, nre, nset, nenergy;
char **groups = NULL;
char groupname[255], fn[255];
int ngroups;
t_rgb rlo, rhi, rmid;
real emax, emid, emin;
real ***emat, **etot, *groupnr;
double beta, expE, **e, *eaver, *efree = NULL, edum;
char label[234];
char **ereflines, **erefres = NULL;
real *eref = NULL, *edif = NULL;
int neref = 0;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
{ efEDR, "-f", NULL, ffOPTRD },
{ efDAT, "-groups", "groups", ffREAD },
{ efDAT, "-eref", "eref", ffOPTRD },
{ efXPM, "-emat", "emat", ffWRITE },
{ efXVG, "-etot", "energy", ffWRITE }
};
#define NFILE asize(fnm)
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;
}
for (i = 0; (i < egNR+egSP); i++)
{
egrp_use[i] = FALSE;
}
egrp_use[egCOULSR] = bCoulSR;
egrp_use[egLJSR] = bLJSR;
egrp_use[egBHAMSR] = bBhamSR;
egrp_use[egCOUL14] = bCoul14;
egrp_use[egLJ14] = bLJ14;
egrp_use[egTotal] = TRUE;
bRef = opt2bSet("-eref", NFILE, fnm);
in = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
do_enxnms(in, &nre, &enm);
if (nre == 0)
{
gmx_fatal(FARGS, "No energies!\n");
}
bCutmax = opt2parg_bSet("-max", asize(pa), pa);
bCutmin = opt2parg_bSet("-min", asize(pa), pa);
nenergy = 0;
/* Read groupnames from input file and construct selection of
energy groups from it*/
fprintf(stderr, "Will read groupnames from inputfile\n");
ngroups = get_lines(opt2fn("-groups", NFILE, fnm), &groups);
fprintf(stderr, "Read %d groups\n", ngroups);
snew(set, static_cast<size_t>(gmx::square(ngroups)*egNR/2));
n = 0;
prevk = 0;
for (i = 0; (i < ngroups); i++)
{
fprintf(stderr, "\rgroup %d", i);
for (j = i; (j < ngroups); j++)
{
for (m = 0; (m < egNR); m++)
{
if (egrp_use[m])
{
sprintf(groupname, "%s:%s-%s", egrp_nm[m], groups[i], groups[j]);
#ifdef DEBUG
fprintf(stderr, "\r%-15s %5d", groupname, n);
#endif
for (k = prevk; (k < prevk+nre); k++)
{
if (std::strcmp(enm[k%nre].name, groupname) == 0)
{
set[n++] = k;
break;
}
}
if (k == prevk+nre)
{
fprintf(stderr, "WARNING! could not find group %s (%d,%d)"
"in energy file\n", groupname, i, j);
}
else
{
prevk = k;
}
}
}
}
}
fprintf(stderr, "\n");
nset = n;
snew(eneset, nset+1);
fprintf(stderr, "Will select half-matrix of energies with %d elements\n", n);
/* Start reading energy frames */
snew(fr, 1);
do
{
do
{
bCont = do_enx(in, fr);
if (bCont)
{
timecheck = check_times(fr->t);
}
}
while (bCont && (timecheck < 0));
if (timecheck == 0)
{
#define DONTSKIP(cnt) (skip) ? ((cnt % skip) == 0) : TRUE
if (bCont)
{
fprintf(stderr, "\rRead frame: %d, Time: %.3f", teller, fr->t);
if ((nenergy % 1000) == 0)
{
srenew(time, nenergy+1000);
for (i = 0; (i <= nset); i++)
{
srenew(eneset[i], nenergy+1000);
}
}
time[nenergy] = fr->t;
sum = 0;
for (i = 0; (i < nset); i++)
{
eneset[i][nenergy] = fr->ener[set[i]].e;
sum += fr->ener[set[i]].e;
}
if (bSum)
{
eneset[nset][nenergy] = sum;
}
nenergy++;
}
teller++;
}
}
while (bCont && (timecheck == 0));
fprintf(stderr, "\n");
fprintf(stderr, "Will build energy half-matrix of %d groups, %d elements, "
"over %d frames\n", ngroups, nset, nenergy);
snew(emat, egNR+egSP);
for (j = 0; (j < egNR+egSP); j++)
{
if (egrp_use[m])
{
snew(emat[j], ngroups);
for (i = 0; (i < ngroups); i++)
{
snew(emat[j][i], ngroups);
}
}
}
snew(groupnr, ngroups);
for (i = 0; (i < ngroups); i++)
{
groupnr[i] = i+1;
}
rlo.r = 1.0, rlo.g = 0.0, rlo.b = 0.0;
rmid.r = 1.0, rmid.g = 1.0, rmid.b = 1.0;
rhi.r = 0.0, rhi.g = 0.0, rhi.b = 1.0;
if (bMeanEmtx)
{
snew(e, ngroups);
for (i = 0; (i < ngroups); i++)
{
snew(e[i], nenergy);
}
n = 0;
for (i = 0; (i < ngroups); i++)
{
for (j = i; (j < ngroups); j++)
{
for (m = 0; (m < egNR); m++)
{
if (egrp_use[m])
{
for (k = 0; (k < nenergy); k++)
{
emat[m][i][j] += eneset[n][k];
e[i][k] += eneset[n][k]; /* *0.5; */
e[j][k] += eneset[n][k]; /* *0.5; */
}
n++;
emat[egTotal][i][j] += emat[m][i][j];
emat[m][i][j] /= nenergy;
emat[m][j][i] = emat[m][i][j];
}
}
emat[egTotal][i][j] /= nenergy;
emat[egTotal][j][i] = emat[egTotal][i][j];
}
}
if (bFree)
{
if (bRef)
{
fprintf(stderr, "Will read reference energies from inputfile\n");
neref = get_lines(opt2fn("-eref", NFILE, fnm), &ereflines);
fprintf(stderr, "Read %d reference energies\n", neref);
snew(eref, neref);
snew(erefres, neref);
for (i = 0; (i < neref); i++)
{
snew(erefres[i], 5);
sscanf(ereflines[i], "%s %lf", erefres[i], &edum);
eref[i] = edum;
}
}
snew(eaver, ngroups);
for (i = 0; (i < ngroups); i++)
{
for (k = 0; (k < nenergy); k++)
{
eaver[i] += e[i][k];
}
eaver[i] /= nenergy;
}
beta = 1.0/(BOLTZ*reftemp);
snew(efree, ngroups);
snew(edif, ngroups);
for (i = 0; (i < ngroups); i++)
{
expE = 0;
for (k = 0; (k < nenergy); k++)
{
expE += std::exp(beta*(e[i][k]-eaver[i]));
}
efree[i] = std::log(expE/nenergy)/beta + eaver[i];
if (bRef)
{
n = search_str2(neref, erefres, groups[i]);
if (n != -1)
{
edif[i] = efree[i]-eref[n];
}
else
{
edif[i] = efree[i];
fprintf(stderr, "WARNING: group %s not found "
"in reference energies.\n", groups[i]);
}
}
else
{
edif[i] = 0;
}
}
}
emid = 0.0; /*(emin+emax)*0.5;*/
egrp_nm[egTotal] = "total";
for (m = 0; (m < egNR+egSP); m++)
{
if (egrp_use[m])
{
emin = 1e10;
emax = -1e10;
for (i = 0; (i < ngroups); i++)
{
for (j = i; (j < ngroups); j++)
{
if (emat[m][i][j] > emax)
{
emax = emat[m][i][j];
}
else if (emat[m][i][j] < emin)
{
emin = emat[m][i][j];
}
}
}
if (emax == emin)
{
fprintf(stderr, "Matrix of %s energy is uniform at %f "
"(will not produce output).\n", egrp_nm[m], emax);
}
else
{
fprintf(stderr, "Matrix of %s energy ranges from %f to %f\n",
egrp_nm[m], emin, emax);
if ((bCutmax) || (emax > cutmax))
{
emax = cutmax;
}
if ((bCutmin) || (emin < cutmin))
{
emin = cutmin;
}
if ((emax == cutmax) || (emin == cutmin))
{
fprintf(stderr, "Energy range adjusted: %f to %f\n", emin, emax);
}
sprintf(fn, "%s%s", egrp_nm[m], ftp2fn(efXPM, NFILE, fnm));
sprintf(label, "%s Interaction Energies", egrp_nm[m]);
out = gmx_ffopen(fn, "w");
if (emin >= emid)
{
write_xpm(out, 0, label, "Energy (kJ/mol)",
"Residue Index", "Residue Index",
ngroups, ngroups, groupnr, groupnr, emat[m],
emid, emax, rmid, rhi, &nlevels);
}
else if (emax <= emid)
{
write_xpm(out, 0, label, "Energy (kJ/mol)",
"Residue Index", "Residue Index",
ngroups, ngroups, groupnr, groupnr, emat[m],
emin, emid, rlo, rmid, &nlevels);
}
else
{
write_xpm3(out, 0, label, "Energy (kJ/mol)",
"Residue Index", "Residue Index",
ngroups, ngroups, groupnr, groupnr, emat[m],
emin, emid, emax, rlo, rmid, rhi, &nlevels);
}
gmx_ffclose(out);
}
}
}
snew(etot, egNR+egSP);
for (m = 0; (m < egNR+egSP); m++)
{
snew(etot[m], ngroups);
for (i = 0; (i < ngroups); i++)
{
for (j = 0; (j < ngroups); j++)
{
etot[m][i] += emat[m][i][j];
}
}
}
out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Mean Energy", "Residue", "kJ/mol",
oenv);
xvgr_legend(out, 0, NULL, oenv);
j = 0;
if (output_env_get_print_xvgr_codes(oenv))
{
char str1[STRLEN], str2[STRLEN];
if (output_env_get_xvg_format(oenv) == exvgXMGR)
{
sprintf(str1, "@ legend string ");
sprintf(str2, " ");
}
else
{
sprintf(str1, "@ s");
sprintf(str2, " legend ");
}
for (m = 0; (m < egNR+egSP); m++)
{
if (egrp_use[m])
{
fprintf(out, "%s%d%s \"%s\"\n", str1, j++, str2, egrp_nm[m]);
}
}
if (bFree)
{
fprintf(out, "%s%d%s \"%s\"\n", str1, j++, str2, "Free");
}
if (bFree)
{
fprintf(out, "%s%d%s \"%s\"\n", str1, j++, str2, "Diff");
}
fprintf(out, "@TYPE xy\n");
fprintf(out, "#%3s", "grp");
for (m = 0; (m < egNR+egSP); m++)
{
if (egrp_use[m])
{
fprintf(out, " %9s", egrp_nm[m]);
}
}
if (bFree)
{
fprintf(out, " %9s", "Free");
}
if (bFree)
{
fprintf(out, " %9s", "Diff");
}
fprintf(out, "\n");
}
for (i = 0; (i < ngroups); i++)
{
fprintf(out, "%3.0f", groupnr[i]);
for (m = 0; (m < egNR+egSP); m++)
{
if (egrp_use[m])
{
fprintf(out, " %9.5g", etot[m][i]);
}
}
if (bFree)
{
fprintf(out, " %9.5g", efree[i]);
}
if (bRef)
{
fprintf(out, " %9.5g", edif[i]);
}
fprintf(out, "\n");
}
xvgrclose(out);
}
else
{
fprintf(stderr, "While typing at your keyboard, suddenly...\n"
"...nothing happens.\nWARNING: Not Implemented Yet\n");
/*
out=ftp2FILE(efMAT,NFILE,fnm,"w");
n=0;
emin=emax=0.0;
for (k=0; (k<nenergy); k++) {
for (i=0; (i<ngroups); i++)
for (j=i+1; (j<ngroups); j++)
emat[i][j]=eneset[n][k];
sprintf(label,"t=%.0f ps",time[k]);
write_matrix(out,ngroups,1,ngroups,groupnr,emat,label,emin,emax,nlevels);
n++;
}
gmx_ffclose(out);
*/
}
close_enx(in);
return 0;
}
int gmx_traj(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] plots coordinates, velocities, forces and/or the box.",
"With [TT]-com[tt] the coordinates, velocities and forces are",
"calculated for the center of mass of each group.",
"When [TT]-mol[tt] is set, the numbers in the index file are",
"interpreted as molecule numbers and the same procedure as with",
"[TT]-com[tt] is used for each molecule.[PAR]",
"Option [TT]-ot[tt] plots the temperature of each group,",
"provided velocities are present in the trajectory file.",
"No corrections are made for constrained degrees of freedom!",
"This implies [TT]-com[tt].[PAR]",
"Options [TT]-ekt[tt] and [TT]-ekr[tt] plot the translational and",
"rotational kinetic energy of each group,",
"provided velocities are present in the trajectory file.",
"This implies [TT]-com[tt].[PAR]",
"Options [TT]-cv[tt] and [TT]-cf[tt] write the average velocities",
"and average forces as temperature factors to a [REF].pdb[ref] file with",
"the average coordinates or the coordinates at [TT]-ctime[tt].",
"The temperature factors are scaled such that the maximum is 10.",
"The scaling can be changed with the option [TT]-scale[tt].",
"To get the velocities or forces of one",
"frame set both [TT]-b[tt] and [TT]-e[tt] to the time of",
"desired frame. When averaging over frames you might need to use",
"the [TT]-nojump[tt] option to obtain the correct average coordinates.",
"If you select either of these option the average force and velocity",
"for each atom are written to an [REF].xvg[ref] file as well",
"(specified with [TT]-av[tt] or [TT]-af[tt]).[PAR]",
"Option [TT]-vd[tt] computes a velocity distribution, i.e. the",
"norm of the vector is plotted. In addition in the same graph",
"the kinetic energy distribution is given."
};
static gmx_bool bMol = FALSE, bCom = FALSE, bPBC = TRUE, bNoJump = FALSE;
static gmx_bool bX = TRUE, bY = TRUE, bZ = TRUE, bNorm = FALSE, bFP = FALSE;
static int ngroups = 1;
static real ctime = -1, scale = 0, binwidth = 1;
t_pargs pa[] = {
{ "-com", FALSE, etBOOL, {&bCom},
"Plot data for the com of each group" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Make molecules whole for COM" },
{ "-mol", FALSE, etBOOL, {&bMol},
"Index contains molecule numbers iso atom numbers" },
{ "-nojump", FALSE, etBOOL, {&bNoJump},
"Remove jumps of atoms across the box" },
{ "-x", FALSE, etBOOL, {&bX},
"Plot X-component" },
{ "-y", FALSE, etBOOL, {&bY},
"Plot Y-component" },
{ "-z", FALSE, etBOOL, {&bZ},
"Plot Z-component" },
{ "-ng", FALSE, etINT, {&ngroups},
"Number of groups to consider" },
{ "-len", FALSE, etBOOL, {&bNorm},
"Plot vector length" },
{ "-fp", FALSE, etBOOL, {&bFP},
"Full precision output" },
{ "-bin", FALSE, etREAL, {&binwidth},
"Binwidth for velocity histogram (nm/ps)" },
{ "-ctime", FALSE, etREAL, {&ctime},
"Use frame at this time for x in [TT]-cv[tt] and [TT]-cf[tt] instead of the average x" },
{ "-scale", FALSE, etREAL, {&scale},
"Scale factor for [REF].pdb[ref] output, 0 is autoscale" }
};
FILE *outx = NULL, *outv = NULL, *outf = NULL, *outb = NULL, *outt = NULL;
FILE *outekt = NULL, *outekr = NULL;
t_topology top;
int ePBC;
real *mass, time;
const char *indexfn;
t_trxframe fr, frout;
int flags, nvhisto = 0, *vhisto = NULL;
rvec *xtop, *xp = NULL;
rvec *sumx = NULL, *sumv = NULL, *sumf = NULL;
matrix topbox;
t_trxstatus *status;
t_trxstatus *status_out = NULL;
gmx_rmpbc_t gpbc = NULL;
int i, j;
int nr_xfr, nr_vfr, nr_ffr;
char **grpname;
int *isize0, *isize;
int **index0, **index;
int *atndx;
t_block *mols;
gmx_bool bTop, bOX, bOXT, bOV, bOF, bOB, bOT, bEKT, bEKR, bCV, bCF;
gmx_bool bDim[4], bDum[4], bVD;
char sffmt[STRLEN], sffmt6[STRLEN];
const char *box_leg[6] = { "XX", "YY", "ZZ", "YX", "ZX", "ZY" };
gmx_output_env_t *oenv;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-ox", "coord", ffOPTWR },
{ efTRX, "-oxt", "coord", ffOPTWR },
{ efXVG, "-ov", "veloc", ffOPTWR },
{ efXVG, "-of", "force", ffOPTWR },
{ efXVG, "-ob", "box", ffOPTWR },
{ efXVG, "-ot", "temp", ffOPTWR },
{ efXVG, "-ekt", "ektrans", ffOPTWR },
{ efXVG, "-ekr", "ekrot", ffOPTWR },
{ efXVG, "-vd", "veldist", ffOPTWR },
{ efPDB, "-cv", "veloc", ffOPTWR },
{ efPDB, "-cf", "force", ffOPTWR },
{ efXVG, "-av", "all_veloc", ffOPTWR },
{ efXVG, "-af", "all_force", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
if (bMol)
{
fprintf(stderr, "Interpreting indexfile entries as molecules.\n"
"Using center of mass.\n");
}
bOX = opt2bSet("-ox", NFILE, fnm);
bOXT = opt2bSet("-oxt", NFILE, fnm);
bOV = opt2bSet("-ov", NFILE, fnm);
bOF = opt2bSet("-of", NFILE, fnm);
bOB = opt2bSet("-ob", NFILE, fnm);
bOT = opt2bSet("-ot", NFILE, fnm);
bEKT = opt2bSet("-ekt", NFILE, fnm);
bEKR = opt2bSet("-ekr", NFILE, fnm);
bCV = opt2bSet("-cv", NFILE, fnm) || opt2bSet("-av", NFILE, fnm);
bCF = opt2bSet("-cf", NFILE, fnm) || opt2bSet("-af", NFILE, fnm);
bVD = opt2bSet("-vd", NFILE, fnm) || opt2parg_bSet("-bin", asize(pa), pa);
if (bMol || bOT || bEKT || bEKR)
{
bCom = TRUE;
}
bDim[XX] = bX;
bDim[YY] = bY;
bDim[ZZ] = bZ;
bDim[DIM] = bNorm;
if (bFP)
{
sprintf(sffmt, "\t%s", gmx_real_fullprecision_pfmt);
}
else
{
sprintf(sffmt, "\t%%g");
}
sprintf(sffmt6, "%s%s%s%s%s%s", sffmt, sffmt, sffmt, sffmt, sffmt, sffmt);
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC,
&xtop, NULL, topbox,
bCom && (bOX || bOXT || bOV || bOT || bEKT || bEKR));
sfree(xtop);
if ((bMol || bCV || bCF) && !bTop)
{
gmx_fatal(FARGS, "Need a run input file for option -mol, -cv or -cf");
}
if (bMol)
{
indexfn = ftp2fn(efNDX, NFILE, fnm);
}
else
{
indexfn = ftp2fn_null(efNDX, NFILE, fnm);
}
if (!(bCom && !bMol))
{
ngroups = 1;
}
snew(grpname, ngroups);
snew(isize0, ngroups);
snew(index0, ngroups);
get_index(&(top.atoms), indexfn, ngroups, isize0, index0, grpname);
if (bMol)
{
mols = &(top.mols);
atndx = mols->index;
ngroups = isize0[0];
snew(isize, ngroups);
snew(index, ngroups);
for (i = 0; i < ngroups; i++)
{
if (index0[0][i] < 0 || index0[0][i] >= mols->nr)
{
gmx_fatal(FARGS, "Molecule index (%d) is out of range (%d-%d)",
index0[0][i]+1, 1, mols->nr);
}
isize[i] = atndx[index0[0][i]+1] - atndx[index0[0][i]];
snew(index[i], isize[i]);
for (j = 0; j < isize[i]; j++)
{
index[i][j] = atndx[index0[0][i]] + j;
}
}
}
else
{
isize = isize0;
index = index0;
}
if (bCom)
{
snew(mass, top.atoms.nr);
for (i = 0; i < top.atoms.nr; i++)
{
mass[i] = top.atoms.atom[i].m;
}
}
else
{
mass = NULL;
}
flags = 0;
if (bOX)
{
flags = flags | TRX_READ_X;
outx = xvgropen(opt2fn("-ox", NFILE, fnm),
bCom ? "Center of mass" : "Coordinate",
output_env_get_xvgr_tlabel(oenv), "Coordinate (nm)", oenv);
make_legend(outx, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOXT)
{
flags = flags | TRX_READ_X;
status_out = open_trx(opt2fn("-oxt", NFILE, fnm), "w");
}
if (bOV)
{
flags = flags | TRX_READ_V;
outv = xvgropen(opt2fn("-ov", NFILE, fnm),
bCom ? "Center of mass velocity" : "Velocity",
output_env_get_xvgr_tlabel(oenv), "Velocity (nm/ps)", oenv);
make_legend(outv, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOF)
{
flags = flags | TRX_READ_F;
outf = xvgropen(opt2fn("-of", NFILE, fnm), "Force",
output_env_get_xvgr_tlabel(oenv), "Force (kJ mol\\S-1\\N nm\\S-1\\N)",
oenv);
make_legend(outf, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOB)
{
outb = xvgropen(opt2fn("-ob", NFILE, fnm), "Box vector elements",
output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
xvgr_legend(outb, 6, box_leg, oenv);
}
if (bOT)
{
bDum[XX] = FALSE;
bDum[YY] = FALSE;
bDum[ZZ] = FALSE;
bDum[DIM] = TRUE;
flags = flags | TRX_READ_V;
outt = xvgropen(opt2fn("-ot", NFILE, fnm), "Temperature",
output_env_get_xvgr_tlabel(oenv), "(K)", oenv);
make_legend(outt, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bEKT)
{
bDum[XX] = FALSE;
bDum[YY] = FALSE;
bDum[ZZ] = FALSE;
bDum[DIM] = TRUE;
flags = flags | TRX_READ_V;
outekt = xvgropen(opt2fn("-ekt", NFILE, fnm), "Center of mass translation",
output_env_get_xvgr_tlabel(oenv), "Energy (kJ mol\\S-1\\N)", oenv);
make_legend(outekt, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bEKR)
{
bDum[XX] = FALSE;
bDum[YY] = FALSE;
bDum[ZZ] = FALSE;
bDum[DIM] = TRUE;
flags = flags | TRX_READ_X | TRX_READ_V;
outekr = xvgropen(opt2fn("-ekr", NFILE, fnm), "Center of mass rotation",
output_env_get_xvgr_tlabel(oenv), "Energy (kJ mol\\S-1\\N)", oenv);
make_legend(outekr, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bVD)
{
flags = flags | TRX_READ_V;
}
if (bCV)
{
flags = flags | TRX_READ_X | TRX_READ_V;
}
if (bCF)
{
flags = flags | TRX_READ_X | TRX_READ_F;
}
if ((flags == 0) && !bOB)
{
fprintf(stderr, "Please select one or more output file options\n");
exit(0);
}
read_first_frame(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &fr, flags);
if ((bOV || bOF) && fn2ftp(ftp2fn(efTRX, NFILE, fnm)) == efXTC)
{
gmx_fatal(FARGS, "Cannot extract velocities or forces since your input XTC file does not contain them.");
}
if (bCV || bCF)
{
snew(sumx, fr.natoms);
}
if (bCV)
{
snew(sumv, fr.natoms);
}
if (bCF)
{
snew(sumf, fr.natoms);
}
nr_xfr = 0;
nr_vfr = 0;
nr_ffr = 0;
if (bCom && bPBC)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, fr.natoms);
}
do
{
time = output_env_conv_time(oenv, fr.time);
if (fr.bX && bNoJump && fr.bBox)
{
if (xp)
{
remove_jump(fr.box, fr.natoms, xp, fr.x);
}
else
{
snew(xp, fr.natoms);
}
for (i = 0; i < fr.natoms; i++)
{
copy_rvec(fr.x[i], xp[i]);
}
}
if (fr.bX && bCom && bPBC)
{
gmx_rmpbc_trxfr(gpbc, &fr);
}
if (bVD && fr.bV)
{
update_histo(isize[0], index[0], fr.v, &nvhisto, &vhisto, binwidth);
}
if (bOX && fr.bX)
{
print_data(outx, time, fr.x, mass, bCom, ngroups, isize, index, bDim, sffmt);
}
if (bOXT && fr.bX)
{
frout = fr;
if (!frout.bAtoms)
{
frout.atoms = &top.atoms;
frout.bAtoms = TRUE;
}
write_trx_x(status_out, &frout, mass, bCom, ngroups, isize, index);
}
if (bOV && fr.bV)
{
print_data(outv, time, fr.v, mass, bCom, ngroups, isize, index, bDim, sffmt);
}
if (bOF && fr.bF)
{
print_data(outf, time, fr.f, NULL, bCom, ngroups, isize, index, bDim, sffmt);
}
if (bOB && fr.bBox)
{
fprintf(outb, "\t%g", fr.time);
fprintf(outb, sffmt6,
fr.box[XX][XX], fr.box[YY][YY], fr.box[ZZ][ZZ],
fr.box[YY][XX], fr.box[ZZ][XX], fr.box[ZZ][YY]);
fprintf(outb, "\n");
}
if (bOT && fr.bV)
{
fprintf(outt, " %g", time);
for (i = 0; i < ngroups; i++)
{
fprintf(outt, sffmt, temp(fr.v, mass, isize[i], index[i]));
}
fprintf(outt, "\n");
}
if (bEKT && fr.bV)
{
fprintf(outekt, " %g", time);
for (i = 0; i < ngroups; i++)
{
fprintf(outekt, sffmt, ektrans(fr.v, mass, isize[i], index[i]));
}
fprintf(outekt, "\n");
}
if (bEKR && fr.bX && fr.bV)
{
fprintf(outekr, " %g", time);
for (i = 0; i < ngroups; i++)
{
fprintf(outekr, sffmt, ekrot(fr.x, fr.v, mass, isize[i], index[i]));
}
fprintf(outekr, "\n");
}
if ((bCV || bCF) && fr.bX &&
(ctime < 0 || (fr.time >= ctime*0.999999 &&
fr.time <= ctime*1.000001)))
{
for (i = 0; i < fr.natoms; i++)
{
rvec_inc(sumx[i], fr.x[i]);
}
nr_xfr++;
}
if (bCV && fr.bV)
{
for (i = 0; i < fr.natoms; i++)
{
rvec_inc(sumv[i], fr.v[i]);
}
nr_vfr++;
}
if (bCF && fr.bF)
{
for (i = 0; i < fr.natoms; i++)
{
rvec_inc(sumf[i], fr.f[i]);
}
nr_ffr++;
}
}
while (read_next_frame(oenv, status, &fr));
if (gpbc != NULL)
{
gmx_rmpbc_done(gpbc);
}
/* clean up a bit */
close_trj(status);
if (bOX)
{
xvgrclose(outx);
}
if (bOXT)
{
close_trx(status_out);
}
if (bOV)
{
xvgrclose(outv);
}
if (bOF)
{
xvgrclose(outf);
}
if (bOB)
{
xvgrclose(outb);
}
if (bOT)
{
xvgrclose(outt);
}
if (bEKT)
{
xvgrclose(outekt);
}
if (bEKR)
{
xvgrclose(outekr);
}
if (bVD)
{
print_histo(opt2fn("-vd", NFILE, fnm), nvhisto, vhisto, binwidth, oenv);
}
if (bCV || bCF)
{
if (nr_xfr > 1)
{
if (ePBC != epbcNONE && !bNoJump)
{
fprintf(stderr, "\nWARNING: More than one frame was used for option -cv or -cf\n"
"If atoms jump across the box you should use the -nojump or -ctime option\n\n");
}
for (i = 0; i < isize[0]; i++)
{
svmul(1.0/nr_xfr, sumx[index[0][i]], sumx[index[0][i]]);
}
}
else if (nr_xfr == 0)
{
fprintf(stderr, "\nWARNING: No coordinate frames found for option -cv or -cf\n\n");
}
}
if (bCV)
{
write_pdb_bfac(opt2fn("-cv", NFILE, fnm),
opt2fn("-av", NFILE, fnm), "average velocity", &(top.atoms),
ePBC, topbox, isize[0], index[0], nr_xfr, sumx,
nr_vfr, sumv, bDim, scale, oenv);
}
if (bCF)
{
write_pdb_bfac(opt2fn("-cf", NFILE, fnm),
opt2fn("-af", NFILE, fnm), "average force", &(top.atoms),
ePBC, topbox, isize[0], index[0], nr_xfr, sumx,
nr_ffr, sumf, bDim, scale, oenv);
}
/* view it */
view_all(oenv, NFILE, fnm);
return 0;
}
void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
real qcut,gmx_bool bSave,real minarea,gmx_bool bPBC,
real dgs_default,gmx_bool bFindex, const output_env_t oenv)
{
FILE *fp,*fp2,*fp3=NULL,*vp;
const char *flegend[] = { "Hydrophobic", "Hydrophilic",
"Total", "D Gsolv" };
const char *vlegend[] = { "Volume (nm\\S3\\N)", "Density (g/l)" };
const char *or_and_oa_legend[] = { "Average (nm\\S2\\N)", "Standard deviation (nm\\S2\\N)" };
const char *vfile;
real t;
gmx_atomprop_t aps=NULL;
gmx_rmpbc_t gpbc=NULL;
t_trxstatus *status;
int ndefault;
int i,j,ii,nfr,natoms,flag,nsurfacedots,res;
rvec *xtop,*x;
matrix topbox,box;
t_topology top;
char title[STRLEN];
int ePBC;
gmx_bool bTop;
t_atoms *atoms;
gmx_bool *bOut,*bPhobic;
gmx_bool bConnelly;
gmx_bool bResAt,bITP,bDGsol;
real *radius,*dgs_factor=NULL,*area=NULL,*surfacedots=NULL;
real at_area,*atom_area=NULL,*atom_area2=NULL;
real *res_a=NULL,*res_area=NULL,*res_area2=NULL;
real totarea,totvolume,totmass=0,density,harea,tarea,fluc2;
atom_id **index,*findex;
int *nx,nphobic,npcheck,retval;
char **grpname,*fgrpname;
real dgsolv;
bITP = opt2bSet("-i",nfile,fnm);
bResAt = opt2bSet("-or",nfile,fnm) || opt2bSet("-oa",nfile,fnm) || bITP;
bTop = read_tps_conf(ftp2fn(efTPS,nfile,fnm),title,&top,&ePBC,
&xtop,NULL,topbox,FALSE);
atoms = &(top.atoms);
if (!bTop) {
fprintf(stderr,"No tpr file, will not compute Delta G of solvation\n");
bDGsol = FALSE;
} else {
bDGsol = strcmp(*(atoms->atomtype[0]),"?") != 0;
if (!bDGsol) {
fprintf(stderr,"Warning: your tpr file is too old, will not compute "
"Delta G of solvation\n");
} else {
printf("In case you use free energy of solvation predictions:\n");
please_cite(stdout,"Eisenberg86a");
}
}
aps = gmx_atomprop_init();
if ((natoms=read_first_x(oenv,&status,ftp2fn(efTRX,nfile,fnm),
&t,&x,box))==0)
gmx_fatal(FARGS,"Could not read coordinates from statusfile\n");
if ((ePBC != epbcXYZ) || (TRICLINIC(box))) {
fprintf(stderr,"\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
"Analysis based on vacuum simulations (with the possibility of evaporation)\n"
"will certainly crash the analysis.\n\n");
}
snew(nx,2);
snew(index,2);
snew(grpname,2);
fprintf(stderr,"Select a group for calculation of surface and a group for output:\n");
get_index(atoms,ftp2fn_null(efNDX,nfile,fnm),2,nx,index,grpname);
if (bFindex) {
fprintf(stderr,"Select a group of hydrophobic atoms:\n");
get_index(atoms,ftp2fn_null(efNDX,nfile,fnm),1,&nphobic,&findex,&fgrpname);
}
snew(bOut,natoms);
for(i=0; i<nx[1]; i++)
bOut[index[1][i]] = TRUE;
/* Now compute atomic readii including solvent probe size */
snew(radius,natoms);
snew(bPhobic,nx[0]);
if (bResAt) {
snew(atom_area,nx[0]);
snew(atom_area2,nx[0]);
snew(res_a,atoms->nres);
snew(res_area,atoms->nres);
snew(res_area2,atoms->nres);
}
if (bDGsol)
snew(dgs_factor,nx[0]);
/* Get a Van der Waals radius for each atom */
ndefault = 0;
for(i=0; (i<natoms); i++) {
if (!gmx_atomprop_query(aps,epropVDW,
*(atoms->resinfo[atoms->atom[i].resind].name),
*(atoms->atomname[i]),&radius[i]))
ndefault++;
/* radius[i] = calc_radius(*(top->atoms.atomname[i])); */
radius[i] += solsize;
}
if (ndefault > 0)
fprintf(stderr,"WARNING: could not find a Van der Waals radius for %d atoms\n",ndefault);
/* Determine which atom is counted as hydrophobic */
if (bFindex) {
npcheck = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
for(j=0; (j<nphobic); j++) {
if (findex[j] == ii) {
bPhobic[i] = TRUE;
if (bOut[ii])
npcheck++;
}
}
}
if (npcheck != nphobic)
gmx_fatal(FARGS,"Consistency check failed: not all %d atoms in the hydrophobic index\n"
"found in the normal index selection (%d atoms)",nphobic,npcheck);
}
else
nphobic = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
if (!bFindex) {
bPhobic[i] = fabs(atoms->atom[ii].q) <= qcut;
if (bPhobic[i] && bOut[ii])
nphobic++;
}
if (bDGsol)
if (!gmx_atomprop_query(aps,epropDGsol,
*(atoms->resinfo[atoms->atom[ii].resind].name),
*(atoms->atomtype[ii]),&(dgs_factor[i])))
dgs_factor[i] = dgs_default;
if (debug)
fprintf(debug,"Atom %5d %5s-%5s: q= %6.3f, r= %6.3f, dgsol= %6.3f, hydrophobic= %s\n",
ii+1,*(atoms->resinfo[atoms->atom[ii].resind].name),
*(atoms->atomname[ii]),
atoms->atom[ii].q,radius[ii]-solsize,dgs_factor[i],
BOOL(bPhobic[i]));
}
fprintf(stderr,"%d out of %d atoms were classified as hydrophobic\n",
nphobic,nx[1]);
fp=xvgropen(opt2fn("-o",nfile,fnm),"Solvent Accessible Surface","Time (ps)",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp,asize(flegend) - (bDGsol ? 0 : 1),flegend,oenv);
vfile = opt2fn_null("-tv",nfile,fnm);
if (vfile) {
if (!bTop) {
gmx_fatal(FARGS,"Need a tpr file for option -tv");
}
vp=xvgropen(vfile,"Volume and Density","Time (ps)","",oenv);
xvgr_legend(vp,asize(vlegend),vlegend,oenv);
totmass = 0;
ndefault = 0;
for(i=0; (i<nx[0]); i++) {
real mm;
ii = index[0][i];
/*
if (!query_atomprop(atomprop,epropMass,
*(top->atoms.resname[top->atoms.atom[ii].resnr]),
*(top->atoms.atomname[ii]),&mm))
ndefault++;
totmass += mm;
*/
totmass += atoms->atom[ii].m;
}
if (ndefault)
fprintf(stderr,"WARNING: Using %d default masses for density calculation, which most likely are inaccurate\n",ndefault);
}
else
vp = NULL;
gmx_atomprop_destroy(aps);
if (bPBC)
gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
nfr=0;
do {
if (bPBC)
gmx_rmpbc(gpbc,natoms,box,x);
bConnelly = (nfr==0 && opt2bSet("-q",nfile,fnm));
if (bConnelly) {
if (!bTop)
gmx_fatal(FARGS,"Need a tpr file for Connelly plot");
flag = FLAG_ATOM_AREA | FLAG_DOTS;
} else {
flag = FLAG_ATOM_AREA;
}
if (vp) {
flag = flag | FLAG_VOLUME;
}
if (debug)
write_sto_conf("check.pdb","pbc check",atoms,x,NULL,ePBC,box);
retval = nsc_dclm_pbc(x,radius,nx[0],ndots,flag,&totarea,
&area,&totvolume,&surfacedots,&nsurfacedots,
index[0],ePBC,bPBC ? box : NULL);
if (retval)
gmx_fatal(FARGS,"Something wrong in nsc_dclm_pbc");
if (bConnelly)
connelly_plot(ftp2fn(efPDB,nfile,fnm),
nsurfacedots,surfacedots,x,atoms,
&(top.symtab),ePBC,box,bSave);
harea = 0;
tarea = 0;
dgsolv = 0;
if (bResAt)
for(i=0; i<atoms->nres; i++)
res_a[i] = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
if (bOut[ii]) {
at_area = area[i];
if (bResAt) {
atom_area[i] += at_area;
atom_area2[i] += sqr(at_area);
res_a[atoms->atom[ii].resind] += at_area;
}
tarea += at_area;
if (bDGsol)
dgsolv += at_area*dgs_factor[i];
if (bPhobic[i])
harea += at_area;
}
}
if (bResAt)
for(i=0; i<atoms->nres; i++) {
res_area[i] += res_a[i];
res_area2[i] += sqr(res_a[i]);
}
fprintf(fp,"%10g %10g %10g %10g",t,harea,tarea-harea,tarea);
if (bDGsol)
fprintf(fp," %10g\n",dgsolv);
else
fprintf(fp,"\n");
/* Print volume */
if (vp) {
density = totmass*AMU/(totvolume*NANO*NANO*NANO);
fprintf(vp,"%12.5e %12.5e %12.5e\n",t,totvolume,density);
}
if (area) {
sfree(area);
area = NULL;
}
if (surfacedots) {
sfree(surfacedots);
surfacedots = NULL;
}
nfr++;
} while (read_next_x(oenv,status,&t,natoms,x,box));
if (bPBC)
gmx_rmpbc_done(gpbc);
fprintf(stderr,"\n");
close_trj(status);
ffclose(fp);
if (vp)
ffclose(vp);
/* if necessary, print areas per atom to file too: */
if (bResAt) {
for(i=0; i<atoms->nres; i++) {
res_area[i] /= nfr;
res_area2[i] /= nfr;
}
for(i=0; i<nx[0]; i++) {
atom_area[i] /= nfr;
atom_area2[i] /= nfr;
}
fprintf(stderr,"Printing out areas per atom\n");
fp = xvgropen(opt2fn("-or",nfile,fnm),"Area per residue over the trajectory","Residue",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp, asize(or_and_oa_legend),or_and_oa_legend,oenv);
fp2 = xvgropen(opt2fn("-oa",nfile,fnm),"Area per atom over the trajectory","Atom #",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp2, asize(or_and_oa_legend),or_and_oa_legend,oenv);
if (bITP) {
fp3 = ftp2FILE(efITP,nfile,fnm,"w");
fprintf(fp3,"[ position_restraints ]\n"
"#define FCX 1000\n"
"#define FCY 1000\n"
"#define FCZ 1000\n"
"; Atom Type fx fy fz\n");
}
for(i=0; i<nx[0]; i++) {
ii = index[0][i];
res = atoms->atom[ii].resind;
if (i==nx[0]-1 || res!=atoms->atom[index[0][i+1]].resind) {
fluc2 = res_area2[res]-sqr(res_area[res]);
if (fluc2 < 0)
fluc2 = 0;
fprintf(fp,"%10d %10g %10g\n",
atoms->resinfo[res].nr,res_area[res],sqrt(fluc2));
}
fluc2 = atom_area2[i]-sqr(atom_area[i]);
if (fluc2 < 0)
fluc2 = 0;
fprintf(fp2,"%d %g %g\n",index[0][i]+1,atom_area[i],sqrt(fluc2));
if (bITP && (atom_area[i] > minarea))
fprintf(fp3,"%5d 1 FCX FCX FCZ\n",ii+1);
}
if (bITP)
ffclose(fp3);
ffclose(fp);
}
/* Be a good citizen, keep our memory free! */
sfree(x);
sfree(nx);
for(i=0;i<2;i++)
{
sfree(index[i]);
sfree(grpname[i]);
}
sfree(bOut);
sfree(radius);
sfree(bPhobic);
if(bResAt)
{
sfree(atom_area);
sfree(atom_area2);
sfree(res_a);
sfree(res_area);
sfree(res_area2);
}
if(bDGsol)
{
sfree(dgs_factor);
}
}
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;
}
double do_tpi(FILE *fplog, t_commrec *cr,
int nfile, const t_filenm fnm[],
const output_env_t oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
int gmx_unused nstglobalcomm,
gmx_vsite_t gmx_unused *vsite, gmx_constr_t gmx_unused constr,
int gmx_unused stepout,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
gmx_membed_t gmx_unused membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
const char gmx_unused *deviceOptions,
int gmx_unused imdport,
unsigned long gmx_unused Flags,
gmx_walltime_accounting_t walltime_accounting)
{
const char *TPI = "Test Particle Insertion";
gmx_localtop_t *top;
gmx_groups_t *groups;
gmx_enerdata_t *enerd;
rvec *f;
real lambda, t, temp, beta, drmax, epot;
double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
t_trxstatus *status;
t_trxframe rerun_fr;
gmx_bool bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS;
tensor force_vir, shake_vir, vir, pres;
int cg_tp, a_tp0, a_tp1, ngid, gid_tp, nener, e;
rvec *x_mol;
rvec mu_tot, x_init, dx, x_tp;
int nnodes, frame;
gmx_int64_t frame_step_prev, frame_step;
gmx_int64_t nsteps, stepblocksize = 0, step;
gmx_int64_t rnd_count_stride, rnd_count;
gmx_int64_t seed;
double rnd[4];
int i, start, end;
FILE *fp_tpi = NULL;
char *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
double dbl, dump_ener;
gmx_bool bCavity;
int nat_cavity = 0, d;
real *mass_cavity = NULL, mass_tot;
int nbin;
double invbinw, *bin, refvolshift, logV, bUlogV;
real dvdl, prescorr, enercorr, dvdlcorr;
gmx_bool bEnergyOutOfBounds;
const char *tpid_leg[2] = {"direct", "reweighted"};
/* Since there is no upper limit to the insertion energies,
* we need to set an upper limit for the distribution output.
*/
real bU_bin_limit = 50;
real bU_logV_bin_limit = bU_bin_limit + 10;
nnodes = cr->nnodes;
top = gmx_mtop_generate_local_top(top_global, inputrec);
groups = &top_global->groups;
bCavity = (inputrec->eI == eiTPIC);
if (bCavity)
{
ptr = getenv("GMX_TPIC_MASSES");
if (ptr == NULL)
{
nat_cavity = 1;
}
else
{
/* Read (multiple) masses from env var GMX_TPIC_MASSES,
* The center of mass of the last atoms is then used for TPIC.
*/
nat_cavity = 0;
while (sscanf(ptr, "%lf%n", &dbl, &i) > 0)
{
srenew(mass_cavity, nat_cavity+1);
mass_cavity[nat_cavity] = dbl;
fprintf(fplog, "mass[%d] = %f\n",
nat_cavity+1, mass_cavity[nat_cavity]);
nat_cavity++;
ptr += i;
}
if (nat_cavity == 0)
{
gmx_fatal(FARGS, "Found %d masses in GMX_TPIC_MASSES", nat_cavity);
}
}
}
/*
init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
/* We never need full pbc for TPI */
fr->ePBC = epbcXYZ;
/* Determine the temperature for the Boltzmann weighting */
temp = inputrec->opts.ref_t[0];
if (fplog)
{
for (i = 1; (i < inputrec->opts.ngtc); i++)
{
if (inputrec->opts.ref_t[i] != temp)
{
fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
}
}
fprintf(fplog,
"\n The temperature for test particle insertion is %.3f K\n\n",
temp);
}
beta = 1.0/(BOLTZ*temp);
/* Number of insertions per frame */
nsteps = inputrec->nsteps;
/* Use the same neighborlist with more insertions points
* in a sphere of radius drmax around the initial point
*/
/* This should be a proper mdp parameter */
drmax = inputrec->rtpi;
/* An environment variable can be set to dump all configurations
* to pdb with an insertion energy <= this value.
*/
dump_pdb = getenv("GMX_TPI_DUMP");
dump_ener = 0;
if (dump_pdb)
{
sscanf(dump_pdb, "%lf", &dump_ener);
}
atoms2md(top_global, inputrec, 0, NULL, top_global->natoms, mdatoms);
update_mdatoms(mdatoms, inputrec->fepvals->init_lambda);
snew(enerd, 1);
init_enerdata(groups->grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd);
snew(f, top_global->natoms);
/* Print to log file */
walltime_accounting_start(walltime_accounting);
wallcycle_start(wcycle, ewcRUN);
print_start(fplog, cr, walltime_accounting, "Test Particle Insertion");
/* The last charge group is the group to be inserted */
cg_tp = top->cgs.nr - 1;
a_tp0 = top->cgs.index[cg_tp];
a_tp1 = top->cgs.index[cg_tp+1];
if (debug)
{
fprintf(debug, "TPI cg %d, atoms %d-%d\n", cg_tp, a_tp0, a_tp1);
}
if (a_tp1 - a_tp0 > 1 &&
(inputrec->rlist < inputrec->rcoulomb ||
inputrec->rlist < inputrec->rvdw))
{
gmx_fatal(FARGS, "Can not do TPI for multi-atom molecule with a twin-range cut-off");
}
snew(x_mol, a_tp1-a_tp0);
bDispCorr = (inputrec->eDispCorr != edispcNO);
bCharge = FALSE;
for (i = a_tp0; i < a_tp1; i++)
{
/* Copy the coordinates of the molecule to be insterted */
copy_rvec(state->x[i], x_mol[i-a_tp0]);
/* Check if we need to print electrostatic energies */
bCharge |= (mdatoms->chargeA[i] != 0 ||
(mdatoms->chargeB && mdatoms->chargeB[i] != 0));
}
bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype != eelRF_NEC);
calc_cgcm(fplog, cg_tp, cg_tp+1, &(top->cgs), state->x, fr->cg_cm);
if (bCavity)
{
if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog)
{
fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
fprintf(stderr, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
}
}
else
{
/* Center the molecule to be inserted at zero */
for (i = 0; i < a_tp1-a_tp0; i++)
{
rvec_dec(x_mol[i], fr->cg_cm[cg_tp]);
}
}
if (fplog)
{
fprintf(fplog, "\nWill insert %d atoms %s partial charges\n",
a_tp1-a_tp0, bCharge ? "with" : "without");
fprintf(fplog, "\nWill insert %d times in each frame of %s\n",
(int)nsteps, opt2fn("-rerun", nfile, fnm));
}
if (!bCavity)
{
if (inputrec->nstlist > 1)
{
if (drmax == 0 && a_tp1-a_tp0 == 1)
{
gmx_fatal(FARGS, "Re-using the neighborlist %d times for insertions of a single atom in a sphere of radius %f does not make sense", inputrec->nstlist, drmax);
}
if (fplog)
{
fprintf(fplog, "Will use the same neighborlist for %d insertions in a sphere of radius %f\n", inputrec->nstlist, drmax);
}
}
}
else
{
if (fplog)
{
fprintf(fplog, "Will insert randomly in a sphere of radius %f around the center of the cavity\n", drmax);
}
}
ngid = groups->grps[egcENER].nr;
gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
nener = 1 + ngid;
if (bDispCorr)
{
nener += 1;
}
if (bCharge)
{
nener += ngid;
if (bRFExcl)
{
nener += 1;
}
if (EEL_FULL(fr->eeltype))
{
nener += 1;
}
}
snew(sum_UgembU, nener);
/* Copy the random seed set by the user */
seed = inputrec->ld_seed;
/* We use the frame step number as one random counter.
* The second counter use the insertion (step) count. But we
* need multiple random numbers per insertion. This number is
* not fixed, since we generate random locations in a sphere
* by putting locations in a cube and some of these fail.
* A count of 20 is already extremely unlikely, so 10000 is
* a safe margin for random numbers per insertion.
*/
rnd_count_stride = 10000;
if (MASTER(cr))
{
fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm),
"TPI energies", "Time (ps)",
"(kJ mol\\S-1\\N) / (nm\\S3\\N)", oenv);
xvgr_subtitle(fp_tpi, "f. are averages over one frame", oenv);
snew(leg, 4+nener);
e = 0;
sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
leg[e++] = strdup(str);
sprintf(str, "f. -kT log<e\\S-\\betaU\\N>");
leg[e++] = strdup(str);
sprintf(str, "f. <e\\S-\\betaU\\N>");
leg[e++] = strdup(str);
sprintf(str, "f. V");
leg[e++] = strdup(str);
sprintf(str, "f. <Ue\\S-\\betaU\\N>");
leg[e++] = strdup(str);
for (i = 0; i < ngid; i++)
{
sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
leg[e++] = strdup(str);
}
if (bDispCorr)
{
sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
leg[e++] = strdup(str);
}
if (bCharge)
{
for (i = 0; i < ngid; i++)
{
sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
leg[e++] = strdup(str);
}
if (bRFExcl)
{
sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
leg[e++] = strdup(str);
}
if (EEL_FULL(fr->eeltype))
{
sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
leg[e++] = strdup(str);
}
}
xvgr_legend(fp_tpi, 4+nener, (const char**)leg, oenv);
for (i = 0; i < 4+nener; i++)
{
sfree(leg[i]);
}
sfree(leg);
}
clear_rvec(x_init);
V_all = 0;
VembU_all = 0;
invbinw = 10;
nbin = 10;
snew(bin, nbin);
/* Avoid frame step numbers <= -1 */
frame_step_prev = -1;
bNotLastFrame = read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm),
&rerun_fr, TRX_NEED_X);
frame = 0;
if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) !=
mdatoms->nr - (a_tp1 - a_tp0))
{
gmx_fatal(FARGS, "Number of atoms in trajectory (%d)%s "
"is not equal the number in the run input file (%d) "
"minus the number of atoms to insert (%d)\n",
rerun_fr.natoms, bCavity ? " minus one" : "",
mdatoms->nr, a_tp1-a_tp0);
}
refvolshift = log(det(rerun_fr.box));
switch (inputrec->eI)
{
case eiTPI:
stepblocksize = inputrec->nstlist;
break;
case eiTPIC:
stepblocksize = 1;
break;
default:
gmx_fatal(FARGS, "Unknown integrator %s", ei_names[inputrec->eI]);
}
#ifdef GMX_SIMD
/* Make sure we don't detect SIMD overflow generated before this point */
gmx_simd_check_and_reset_overflow();
#endif
while (bNotLastFrame)
{
frame_step = rerun_fr.step;
if (frame_step <= frame_step_prev)
{
/* We don't have step number in the trajectory file,
* or we have constant or decreasing step numbers.
* Ensure we have increasing step numbers, since we use
* the step numbers as a counter for random numbers.
*/
frame_step = frame_step_prev + 1;
}
frame_step_prev = frame_step;
lambda = rerun_fr.lambda;
t = rerun_fr.time;
sum_embU = 0;
for (e = 0; e < nener; e++)
{
sum_UgembU[e] = 0;
}
/* Copy the coordinates from the input trajectory */
for (i = 0; i < rerun_fr.natoms; i++)
{
copy_rvec(rerun_fr.x[i], state->x[i]);
}
copy_mat(rerun_fr.box, state->box);
V = det(state->box);
logV = log(V);
bStateChanged = TRUE;
bNS = TRUE;
step = cr->nodeid*stepblocksize;
while (step < nsteps)
{
/* Initialize the second counter for random numbers using
* the insertion step index. This ensures that we get
* the same random numbers independently of how many
* MPI ranks we use. Also for the same seed, we get
* the same initial random sequence for different nsteps.
*/
rnd_count = step*rnd_count_stride;
if (!bCavity)
{
/* Random insertion in the whole volume */
bNS = (step % inputrec->nstlist == 0);
if (bNS)
{
/* Generate a random position in the box */
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
for (d = 0; d < DIM; d++)
{
x_init[d] = rnd[d]*state->box[d][d];
}
}
if (inputrec->nstlist == 1)
{
copy_rvec(x_init, x_tp);
}
else
{
/* Generate coordinates within |dx|=drmax of x_init */
do
{
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
for (d = 0; d < DIM; d++)
{
dx[d] = (2*rnd[d] - 1)*drmax;
}
}
while (norm2(dx) > drmax*drmax);
rvec_add(x_init, dx, x_tp);
}
}
else
{
/* Random insertion around a cavity location
* given by the last coordinate of the trajectory.
*/
if (step == 0)
{
if (nat_cavity == 1)
{
/* Copy the location of the cavity */
copy_rvec(rerun_fr.x[rerun_fr.natoms-1], x_init);
}
else
{
/* Determine the center of mass of the last molecule */
clear_rvec(x_init);
mass_tot = 0;
for (i = 0; i < nat_cavity; i++)
{
for (d = 0; d < DIM; d++)
{
x_init[d] +=
mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
}
mass_tot += mass_cavity[i];
}
for (d = 0; d < DIM; d++)
{
x_init[d] /= mass_tot;
}
}
}
/* Generate coordinates within |dx|=drmax of x_init */
do
{
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
for (d = 0; d < DIM; d++)
{
dx[d] = (2*rnd[d] - 1)*drmax;
}
}
while (norm2(dx) > drmax*drmax);
rvec_add(x_init, dx, x_tp);
}
if (a_tp1 - a_tp0 == 1)
{
/* Insert a single atom, just copy the insertion location */
copy_rvec(x_tp, state->x[a_tp0]);
}
else
{
/* Copy the coordinates from the top file */
for (i = a_tp0; i < a_tp1; i++)
{
copy_rvec(x_mol[i-a_tp0], state->x[i]);
}
/* Rotate the molecule randomly */
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
rotate_conf(a_tp1-a_tp0, state->x+a_tp0, NULL,
2*M_PI*rnd[0],
2*M_PI*rnd[1],
2*M_PI*rnd[2]);
/* Shift to the insertion location */
for (i = a_tp0; i < a_tp1; i++)
{
rvec_inc(state->x[i], x_tp);
}
}
/* Clear some matrix variables */
clear_mat(force_vir);
clear_mat(shake_vir);
clear_mat(vir);
clear_mat(pres);
/* Set the charge group center of mass of the test particle */
copy_rvec(x_init, fr->cg_cm[top->cgs.nr-1]);
/* Calc energy (no forces) on new positions.
* Since we only need the intermolecular energy
* and the RF exclusion terms of the inserted molecule occur
* within a single charge group we can pass NULL for the graph.
* This also avoids shifts that would move charge groups
* out of the box.
*
* Some checks above ensure than we can not have
* twin-range interactions together with nstlist > 1,
* therefore we do not need to remember the LR energies.
*/
/* Make do_force do a single node force calculation */
cr->nnodes = 1;
do_force(fplog, cr, inputrec,
step, nrnb, wcycle, top, &top_global->groups,
state->box, state->x, &state->hist,
f, force_vir, mdatoms, enerd, fcd,
state->lambda,
NULL, fr, NULL, mu_tot, t, NULL, NULL, FALSE,
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
(bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS | GMX_FORCE_DO_LR : 0) |
(bStateChanged ? GMX_FORCE_STATECHANGED : 0));
cr->nnodes = nnodes;
bStateChanged = FALSE;
bNS = FALSE;
/* Calculate long range corrections to pressure and energy */
calc_dispcorr(fplog, inputrec, fr, step, top_global->natoms, state->box,
lambda, pres, vir, &prescorr, &enercorr, &dvdlcorr);
/* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
enerd->term[F_DISPCORR] = enercorr;
enerd->term[F_EPOT] += enercorr;
enerd->term[F_PRES] += prescorr;
enerd->term[F_DVDL_VDW] += dvdlcorr;
epot = enerd->term[F_EPOT];
bEnergyOutOfBounds = FALSE;
#ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
/* With SSE the energy can overflow, check for this */
if (gmx_mm_check_and_reset_overflow())
{
if (debug)
{
fprintf(debug, "Found an SSE overflow, assuming the energy is out of bounds\n");
}
bEnergyOutOfBounds = TRUE;
}
#endif
/* If the compiler doesn't optimize this check away
* we catch the NAN energies.
* The epot>GMX_REAL_MAX check catches inf values,
* which should nicely result in embU=0 through the exp below,
* but it does not hurt to check anyhow.
*/
/* Non-bonded Interaction usually diverge at r=0.
* With tabulated interaction functions the first few entries
* should be capped in a consistent fashion between
* repulsion, dispersion and Coulomb to avoid accidental
* negative values in the total energy.
* The table generation code in tables.c does this.
* With user tbales the user should take care of this.
*/
if (epot != epot || epot > GMX_REAL_MAX)
{
bEnergyOutOfBounds = TRUE;
}
if (bEnergyOutOfBounds)
{
if (debug)
{
fprintf(debug, "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t, (int)step, epot);
}
embU = 0;
}
else
{
embU = exp(-beta*epot);
sum_embU += embU;
/* Determine the weighted energy contributions of each energy group */
e = 0;
sum_UgembU[e++] += epot*embU;
if (fr->bBHAM)
{
for (i = 0; i < ngid; i++)
{
sum_UgembU[e++] +=
(enerd->grpp.ener[egBHAMSR][GID(i, gid_tp, ngid)] +
enerd->grpp.ener[egBHAMLR][GID(i, gid_tp, ngid)])*embU;
}
}
else
{
for (i = 0; i < ngid; i++)
{
sum_UgembU[e++] +=
(enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] +
enerd->grpp.ener[egLJLR][GID(i, gid_tp, ngid)])*embU;
}
}
if (bDispCorr)
{
sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
}
if (bCharge)
{
for (i = 0; i < ngid; i++)
{
sum_UgembU[e++] +=
(enerd->grpp.ener[egCOULSR][GID(i, gid_tp, ngid)] +
enerd->grpp.ener[egCOULLR][GID(i, gid_tp, ngid)])*embU;
}
if (bRFExcl)
{
sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
}
if (EEL_FULL(fr->eeltype))
{
sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
}
}
}
if (embU == 0 || beta*epot > bU_bin_limit)
{
bin[0]++;
}
else
{
i = (int)((bU_logV_bin_limit
- (beta*epot - logV + refvolshift))*invbinw
+ 0.5);
if (i < 0)
{
i = 0;
}
if (i >= nbin)
{
realloc_bins(&bin, &nbin, i+10);
}
bin[i]++;
}
if (debug)
{
fprintf(debug, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
(int)step, epot, x_tp[XX], x_tp[YY], x_tp[ZZ]);
}
if (dump_pdb && epot <= dump_ener)
{
sprintf(str, "t%g_step%d.pdb", t, (int)step);
sprintf(str2, "t: %f step %d ener: %f", t, (int)step, epot);
write_sto_conf_mtop(str, str2, top_global, state->x, state->v,
inputrec->ePBC, state->box);
}
step++;
if ((step/stepblocksize) % cr->nnodes != cr->nodeid)
{
/* Skip all steps assigned to the other MPI ranks */
step += (cr->nnodes - 1)*stepblocksize;
}
}
if (PAR(cr))
{
/* When running in parallel sum the energies over the processes */
gmx_sumd(1, &sum_embU, cr);
gmx_sumd(nener, sum_UgembU, cr);
}
frame++;
V_all += V;
VembU_all += V*sum_embU/nsteps;
if (fp_tpi)
{
if (bVerbose || frame%10 == 0 || frame < 10)
{
fprintf(stderr, "mu %10.3e <mu> %10.3e\n",
-log(sum_embU/nsteps)/beta, -log(VembU_all/V_all)/beta);
}
fprintf(fp_tpi, "%10.3f %12.5e %12.5e %12.5e %12.5e",
t,
VembU_all == 0 ? 20/beta : -log(VembU_all/V_all)/beta,
sum_embU == 0 ? 20/beta : -log(sum_embU/nsteps)/beta,
sum_embU/nsteps, V);
for (e = 0; e < nener; e++)
{
fprintf(fp_tpi, " %12.5e", sum_UgembU[e]/nsteps);
}
fprintf(fp_tpi, "\n");
fflush(fp_tpi);
}
bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
} /* End of the loop */
walltime_accounting_end(walltime_accounting);
close_trj(status);
if (fp_tpi != NULL)
{
gmx_fio_fclose(fp_tpi);
}
if (fplog != NULL)
{
fprintf(fplog, "\n");
fprintf(fplog, " <V> = %12.5e nm^3\n", V_all/frame);
fprintf(fplog, " <mu> = %12.5e kJ/mol\n", -log(VembU_all/V_all)/beta);
}
/* Write the Boltzmann factor histogram */
if (PAR(cr))
{
/* When running in parallel sum the bins over the processes */
i = nbin;
global_max(cr, &i);
realloc_bins(&bin, &nbin, i);
gmx_sumd(nbin, bin, cr);
}
if (MASTER(cr))
{
fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm),
"TPI energy distribution",
"\\betaU - log(V/<V>)", "count", oenv);
sprintf(str, "number \\betaU > %g: %9.3e", bU_bin_limit, bin[0]);
xvgr_subtitle(fp_tpi, str, oenv);
xvgr_legend(fp_tpi, 2, (const char **)tpid_leg, oenv);
for (i = nbin-1; i > 0; i--)
{
bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
fprintf(fp_tpi, "%6.2f %10d %12.5e\n",
bUlogV,
(int)(bin[i]+0.5),
bin[i]*exp(-bUlogV)*V_all/VembU_all);
}
gmx_fio_fclose(fp_tpi);
}
sfree(bin);
sfree(sum_UgembU);
walltime_accounting_set_nsteps_done(walltime_accounting, frame*inputrec->nsteps);
return 0;
}
extern FILE *open_dhdl(const char *filename, const t_inputrec *ir,
const gmx_output_env_t *oenv)
{
FILE *fp;
const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
*lambdastate = "\\lambda state";
char title[STRLEN], label_x[STRLEN], label_y[STRLEN];
int i, nps, nsets, nsets_de, nsetsbegin;
int n_lambda_terms = 0;
t_lambda *fep = ir->fepvals; /* for simplicity */
t_expanded *expand = ir->expandedvals;
char **setname;
char buf[STRLEN], lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
int bufplace = 0;
int nsets_dhdl = 0;
int s = 0;
int nsetsextend;
gmx_bool write_pV = FALSE;
/* count the number of different lambda terms */
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
n_lambda_terms++;
}
}
if (fep->n_lambda == 0)
{
sprintf(title, "%s", dhdl);
sprintf(label_x, "Time (ps)");
sprintf(label_y, "%s (%s %s)",
dhdl, unit_energy, "[\\lambda]\\S-1\\N");
}
else
{
sprintf(title, "%s and %s", dhdl, deltag);
sprintf(label_x, "Time (ps)");
sprintf(label_y, "%s and %s (%s %s)",
dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N");
}
fp = gmx_fio_fopen(filename, "w+");
xvgr_header(fp, title, label_x, label_y, exvggtXNY, oenv);
if (!(ir->bSimTemp))
{
bufplace = sprintf(buf, "T = %g (K) ",
ir->opts.ref_t[0]);
}
if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
{
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* compatibility output */
sprintf(&(buf[bufplace]), "%s = %.4f", lambda, fep->init_lambda);
}
else
{
print_lambda_vector(fep, fep->init_fep_state, TRUE, FALSE,
lambda_vec_str);
print_lambda_vector(fep, fep->init_fep_state, TRUE, TRUE,
lambda_name_str);
sprintf(&(buf[bufplace]), "%s %d: %s = %s",
lambdastate, fep->init_fep_state,
lambda_name_str, lambda_vec_str);
}
}
xvgr_subtitle(fp, buf, oenv);
nsets_dhdl = 0;
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
nsets_dhdl = n_lambda_terms;
}
/* count the number of delta_g states */
nsets_de = fep->lambda_stop_n - fep->lambda_start_n;
nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
{
nsets += 1; /*add fep state for expanded ensemble */
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
{
nsetsextend += 1; /* for PV term, other terms possible if required for
the reduced potential (only needed with foreign
lambda, and only output when init_lambda is not
set in order to maintain compatibility of the
dhdl.xvg file) */
write_pV = TRUE;
}
snew(setname, nsetsextend);
if (expand->elmcmove > elmcmoveNO)
{
/* state for the fep_vals, if we have alchemical sampling */
sprintf(buf, "%s", "Thermodynamic state");
setname[s] = gmx_strdup(buf);
s += 1;
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
switch (fep->edHdLPrintEnergy)
{
case edHdLPrintEnergyPOTENTIAL:
sprintf(buf, "%s (%s)", "Potential Energy", unit_energy);
break;
case edHdLPrintEnergyTOTAL:
case edHdLPrintEnergyYES:
default:
sprintf(buf, "%s (%s)", "Total Energy", unit_energy);
}
setname[s] = gmx_strdup(buf);
s += 1;
}
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* compatibility output */
sprintf(buf, "%s %s %.4f", dhdl, lambda, fep->init_lambda);
}
else
{
double lam = fep->init_lambda;
if (fep->init_lambda < 0)
{
lam = fep->all_lambda[i][fep->init_fep_state];
}
sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i],
lam);
}
setname[s] = gmx_strdup(buf);
s += 1;
}
}
}
if (fep->n_lambda > 0)
{
/* g_bar has to determine the lambda values used in this simulation
* from this xvg legend.
*/
if (expand->elmcmove > elmcmoveNO)
{
nsetsbegin = 1; /* for including the expanded ensemble */
}
else
{
nsetsbegin = 0;
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsetsbegin += 1;
}
nsetsbegin += nsets_dhdl;
for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
{
print_lambda_vector(fep, i, FALSE, FALSE, lambda_vec_str);
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* for compatible dhdl.xvg files */
nps = sprintf(buf, "%s %s %s", deltag, lambda, lambda_vec_str);
}
else
{
nps = sprintf(buf, "%s %s to %s", deltag, lambda, lambda_vec_str);
}
if (ir->bSimTemp)
{
/* print the temperature for this state if doing simulated annealing */
sprintf(&buf[nps], "T = %g (%s)",
ir->simtempvals->temperatures[s-(nsetsbegin)],
unit_temp_K);
}
setname[s] = gmx_strdup(buf);
s++;
}
if (write_pV)
{
sprintf(buf, "pV (%s)", unit_energy);
setname[nsetsextend-1] = gmx_strdup(buf); /* the first entry after
nsets */
}
xvgr_legend(fp, nsetsextend, (const char **)setname, oenv);
for (s = 0; s < nsetsextend; s++)
{
sfree(setname[s]);
}
sfree(setname);
}
return fp;
}
void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
const output_env_t oenv)
{
FILE *fp;
t_mapping *map;
int f, r, *count, *total, ss_count, total_count;
size_t s;
const char** leg;
map = mat->map;
snew(count, mat->nmap);
snew(total, mat->nmap);
snew(leg, mat->nmap+1);
leg[0] = "Structure";
for (s = 0; s < (size_t)mat->nmap; s++)
{
leg[s+1] = gmx_strdup(map[s].desc);
}
fp = xvgropen(outfile, "Secondary Structure",
output_env_get_xvgr_tlabel(oenv), "Number of Residues", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"Structure = ");
}
for (s = 0; s < strlen(ss_string); s++)
{
if (s > 0)
{
fprintf(fp, " + ");
}
for (f = 0; f < mat->nmap; f++)
{
if (ss_string[s] == map[f].code.c1)
{
fprintf(fp, "%s", map[f].desc);
}
}
}
fprintf(fp, "\"\n");
xvgr_legend(fp, mat->nmap+1, leg, oenv);
total_count = 0;
for (s = 0; s < (size_t)mat->nmap; s++)
{
total[s] = 0;
}
for (f = 0; f < mat->nx; f++)
{
ss_count = 0;
for (s = 0; s < (size_t)mat->nmap; s++)
{
count[s] = 0;
}
for (r = 0; r < mat->ny; r++)
{
count[mat->matrix[f][r]]++;
total[mat->matrix[f][r]]++;
}
for (s = 0; s < (size_t)mat->nmap; s++)
{
if (strchr(ss_string, map[s].code.c1))
{
ss_count += count[s];
total_count += count[s];
}
}
fprintf(fp, "%8g %5d", mat->axis_x[f], ss_count);
for (s = 0; s < (size_t)mat->nmap; s++)
{
fprintf(fp, " %5d", count[s]);
}
fprintf(fp, "\n");
}
/* now print column totals */
fprintf(fp, "%-8s %5d", "# Totals", total_count);
for (s = 0; s < (size_t)mat->nmap; s++)
{
fprintf(fp, " %5d", total[s]);
}
fprintf(fp, "\n");
/* now print percentages */
fprintf(fp, "%-8s %5.2f", "# SS %", total_count / (real) (mat->nx * mat->ny));
for (s = 0; s < (size_t)mat->nmap; s++)
{
fprintf(fp, " %5.2f", total[s] / (real) (mat->nx * mat->ny));
}
fprintf(fp, "\n");
xvgrclose(fp);
sfree(leg);
sfree(count);
}
int gmx_sigeps(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_sigeps[tt] is a simple utility that converts C6/C12 or C6/Cn combinations",
"to [GRK]sigma[grk] and [GRK]epsilon[grk], or vice versa. It can also plot the potential",
"in file. In addition, it makes an approximation of a Buckingham potential",
"to a Lennard-Jones potential."
};
static real c6 = 1.0e-3, cn = 1.0e-6, qi = 0, qj = 0, sig = 0.3, eps = 1, sigfac = 0.7;
static real Abh = 1e5, Bbh = 32, Cbh = 1e-3;
static int npow = 12;
t_pargs pa[] = {
{ "-c6", FALSE, etREAL, {&c6}, "C6" },
{ "-cn", FALSE, etREAL, {&cn}, "Constant for repulsion" },
{ "-pow", FALSE, etINT, {&npow}, "Power of the repulsion term" },
{ "-sig", FALSE, etREAL, {&sig}, "[GRK]sigma[grk]" },
{ "-eps", FALSE, etREAL, {&eps}, "[GRK]epsilon[grk]" },
{ "-A", FALSE, etREAL, {&Abh}, "Buckingham A" },
{ "-B", FALSE, etREAL, {&Bbh}, "Buckingham B" },
{ "-C", FALSE, etREAL, {&Cbh}, "Buckingham C" },
{ "-qi", FALSE, etREAL, {&qi}, "qi" },
{ "-qj", FALSE, etREAL, {&qj}, "qj" },
{ "-sigfac", FALSE, etREAL, {&sigfac}, "Factor in front of [GRK]sigma[grk] for starting the plot" }
};
t_filenm fnm[] = {
{ efXVG, "-o", "potje", ffWRITE }
};
output_env_t oenv;
#define NFILE asize(fnm)
const char *legend[] = { "Lennard-Jones", "Buckingham" };
FILE *fp;
int i;
gmx_bool bBham;
real qq, x, oldx, minimum, mval, dp[2], pp[2];
int cur = 0;
#define next (1-cur)
parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc),
desc, 0, NULL, &oenv);
bBham = (opt2parg_bSet("-A", asize(pa), pa) ||
opt2parg_bSet("-B", asize(pa), pa) ||
opt2parg_bSet("-C", asize(pa), pa));
if (bBham)
{
c6 = Cbh;
sig = pow((6.0/npow)*pow(npow/Bbh, npow-6.0), 1.0/(npow-6.0));
eps = c6/(4*pow(sig, 6.0));
cn = 4*eps*pow(sig, npow);
}
else
{
if (opt2parg_bSet("-sig", asize(pa), pa) ||
opt2parg_bSet("-eps", asize(pa), pa))
{
c6 = 4*eps*pow(sig, 6);
cn = 4*eps*pow(sig, npow);
}
else if (opt2parg_bSet("-c6", asize(pa), pa) ||
opt2parg_bSet("-cn", asize(pa), pa) ||
opt2parg_bSet("-pow", asize(pa), pa))
{
sig = pow(cn/c6, 1.0/(npow-6.0));
eps = 0.25*c6*pow(sig, -6.0);
}
else
{
sig = eps = 0;
}
printf("c6 = %12.5e, c%d = %12.5e\n", c6, npow, cn);
printf("sigma = %12.5f, epsilon = %12.5f\n", sig, eps);
minimum = pow(npow/6.0*pow(sig, npow-6.0), 1.0/(npow-6));
printf("Van der Waals minimum at %g, V = %g\n\n",
minimum, pot(minimum, 0, c6, cn, npow));
printf("Fit of Lennard Jones (%d-6) to Buckingham:\n", npow);
Bbh = npow/minimum;
Cbh = c6;
Abh = 4*eps*pow(sig/minimum, npow)*exp(npow);
printf("A = %g, B = %g, C = %g\n", Abh, Bbh, Cbh);
}
qq = qi*qj;
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Potential", "r (nm)", "E (kJ/mol)",
oenv);
xvgr_legend(fp, asize(legend), legend,
oenv);
if (sig == 0)
{
sig = 0.25;
}
minimum = -1;
mval = 0;
oldx = 0;
for (i = 0; (i < 100); i++)
{
x = sigfac*sig+sig*i*0.02;
dp[next] = dpot(x, qq, c6, cn, npow);
fprintf(fp, "%10g %10g %10g\n", x, pot(x, qq, c6, cn, npow),
bhpot(x, Abh, Bbh, Cbh));
if (qq != 0)
{
if ((i > 0) && (dp[cur]*dp[next] < 0))
{
minimum = oldx + dp[cur]*(x-oldx)/(dp[cur]-dp[next]);
mval = pot(minimum, qq, c6, cn, npow);
printf("Van der Waals + Coulomb minimum at r = %g (nm). Value = %g (kJ/mol)\n",
minimum, mval);
}
}
cur = next;
oldx = x;
}
ffclose(fp);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
return 0;
}
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_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_vanhove(int argc,char *argv[])
{
const char *desc[] = {
"g_vanhove computes the Van Hove correlation function.",
"The Van Hove G(r,t) is the probability that a particle that is at r0",
"at time zero can be found at position r0+r at time t.",
"g_vanhove determines G not for a vector r, but for the length of r.",
"Thus it gives the probability that a particle moves a distance of r",
"in time t.",
"Jumps across the periodic boundaries are removed.",
"Corrections are made for scaling due to isotropic",
"or anisotropic pressure coupling.",
"[PAR]",
"With option [TT]-om[tt] the whole matrix can be written as a function",
"of t and r or as a function of sqrt(t) and r (option [TT]-sqrt[tt]).",
"[PAR]",
"With option [TT]-or[tt] the Van Hove function is plotted for one",
"or more values of t. Option [TT]-nr[tt] sets the number of times,",
"option [TT]-fr[tt] the number spacing between the times.",
"The binwidth is set with option [TT]-rbin[tt]. The number of bins",
"is determined automatically.",
"[PAR]",
"With option [TT]-ot[tt] the integral up to a certain distance",
"(option [TT]-rt[tt]) is plotted as a function of time.",
"[PAR]",
"For all frames that are read the coordinates of the selected particles",
"are stored in memory. Therefore the program may use a lot of memory.",
"For options [TT]-om[tt] and [TT]-ot[tt] the program may be slow.",
"This is because the calculation scales as the number of frames times",
"[TT]-fm[tt] or [TT]-ft[tt].",
"Note that with the [TT]-dt[tt] option the memory usage and calculation",
"time can be reduced."
};
static int fmmax=0,ftmax=0,nlev=81,nr=1,fshift=0;
static real sbin=0,rmax=2,rbin=0.01,mmax=0,rint=0;
t_pargs pa[] = {
{ "-sqrt", FALSE, etREAL,{&sbin},
"Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)" },
{ "-fm", FALSE, etINT, {&fmmax},
"Number of frames in the matrix, 0 is plot all" },
{ "-rmax", FALSE, etREAL, {&rmax},
"Maximum r in the matrix (nm)" },
{ "-rbin", FALSE, etREAL, {&rbin},
"Binwidth in the matrix and for -or (nm)" },
{ "-mmax", FALSE, etREAL, {&mmax},
"Maximum density in the matrix, 0 is calculate (1/nm)" },
{ "-nlevels" ,FALSE, etINT, {&nlev},
"Number of levels in the matrix" },
{ "-nr", FALSE, etINT, {&nr},
"Number of curves for the -or output" },
{ "-fr", FALSE, etINT, {&fshift},
"Frame spacing for the -or output" },
{ "-rt", FALSE, etREAL, {&rint},
"Integration limit for the -ot output (nm)" },
{ "-ft", FALSE, etINT, {&ftmax},
"Number of frames in the -ot output, 0 is plot all" }
};
#define NPA asize(pa)
t_filenm fnm[] = {
{ efTRX, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXPM, "-om", "vanhove", ffOPTWR },
{ efXVG, "-or", "vanhove_r", ffOPTWR },
{ efXVG, "-ot", "vanhove_t", ffOPTWR }
};
#define NFILE asize(fnm)
output_env_t oenv;
const char *matfile,*otfile,*orfile;
char title[256];
t_topology top;
int ePBC;
matrix boxtop,box,*sbox,avbox,corr;
rvec *xtop,*x,**sx;
int isize,nalloc,nallocn,natom;
t_trxstatus *status;
atom_id *index;
char *grpname;
int nfr,f,ff,i,m,mat_nx=0,nbin=0,bin,mbin,fbin;
real *time,t,invbin=0,rmax2=0,rint2=0,d2;
real invsbin=0,matmax,normfac,dt,*tickx,*ticky;
char buf[STRLEN],**legend;
real **mat=NULL;
int *pt=NULL,**pr=NULL,*mcount=NULL,*tcount=NULL,*rcount=NULL;
FILE *fp;
t_rgb rlo={1,1,1}, rhi={0,0,0};
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
matfile = opt2fn_null("-om",NFILE,fnm);
if (opt2parg_bSet("-fr",NPA,pa))
orfile = opt2fn("-or",NFILE,fnm);
else
orfile = opt2fn_null("-or",NFILE,fnm);
if (opt2parg_bSet("-rt",NPA,pa))
otfile = opt2fn("-ot",NFILE,fnm);
else
otfile = opt2fn_null("-ot",NFILE,fnm);
if (!matfile && !otfile && !orfile) {
fprintf(stderr,
"For output set one (or more) of the output file options\n");
exit(0);
}
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,boxtop,
FALSE);
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
nalloc = 0;
time = NULL;
sbox = NULL;
sx = NULL;
clear_mat(avbox);
natom=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
nfr = 0;
do {
if (nfr >= nalloc) {
nalloc += 100;
srenew(time,nalloc);
srenew(sbox,nalloc);
srenew(sx,nalloc);
}
time[nfr] = t;
copy_mat(box,sbox[nfr]);
/* This assumes that the off-diagonal box elements
* are not affected by jumps across the periodic boundaries.
*/
m_add(avbox,box,avbox);
snew(sx[nfr],isize);
for(i=0; i<isize; i++)
copy_rvec(x[index[i]],sx[nfr][i]);
nfr++;
} while (read_next_x(oenv,status,&t,natom,x,box));
/* clean up */
sfree(x);
close_trj(status);
fprintf(stderr,"Read %d frames\n",nfr);
dt = (time[nfr-1] - time[0])/(nfr - 1);
/* Some ugly rounding to get nice nice times in the output */
dt = (int)(10000.0*dt + 0.5)/10000.0;
invbin = 1.0/rbin;
if (matfile) {
if (fmmax <= 0 || fmmax >= nfr)
fmmax = nfr - 1;
snew(mcount,fmmax);
nbin = (int)(rmax*invbin + 0.5);
if (sbin == 0) {
mat_nx = fmmax + 1;
} else {
invsbin = 1.0/sbin;
mat_nx = sqrt(fmmax*dt)*invsbin + 1;
}
snew(mat,mat_nx);
for(f=0; f<mat_nx; f++)
snew(mat[f],nbin);
rmax2 = sqr(nbin*rbin);
/* Initialize time zero */
mat[0][0] = nfr*isize;
mcount[0] += nfr;
} else {
fmmax = 0;
}
if (orfile) {
snew(pr,nr);
nalloc = 0;
snew(rcount,nr);
}
if (otfile) {
if (ftmax <= 0)
ftmax = nfr - 1;
snew(tcount,ftmax);
snew(pt,nfr);
rint2 = rint*rint;
/* Initialize time zero */
pt[0] = nfr*isize;
tcount[0] += nfr;
} else {
ftmax = 0;
}
msmul(avbox,1.0/nfr,avbox);
for(f=0; f<nfr; f++) {
if (f % 100 == 0)
fprintf(stderr,"\rProcessing frame %d",f);
/* Scale all the configuration to the average box */
m_inv_ur0(sbox[f],corr);
mmul_ur0(avbox,corr,corr);
for(i=0; i<isize; i++) {
mvmul_ur0(corr,sx[f][i],sx[f][i]);
if (f > 0) {
/* Correct for periodic jumps */
for(m=DIM-1; m>=0; m--) {
while(sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
rvec_dec(sx[f][i],avbox[m]);
while(sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
rvec_inc(sx[f][i],avbox[m]);
}
}
}
for(ff=0; ff<f; ff++) {
fbin = f - ff;
if (fbin <= fmmax || fbin <= ftmax) {
if (sbin == 0)
mbin = fbin;
else
mbin = (int)(sqrt(fbin*dt)*invsbin + 0.5);
for(i=0; i<isize; i++) {
d2 = distance2(sx[f][i],sx[ff][i]);
if (mbin < mat_nx && d2 < rmax2) {
bin = (int)(sqrt(d2)*invbin + 0.5);
if (bin < nbin) {
mat[mbin][bin] += 1;
}
}
if (fbin <= ftmax && d2 <= rint2)
pt[fbin]++;
}
if (matfile)
mcount[mbin]++;
if (otfile)
tcount[fbin]++;
}
}
if (orfile) {
for(fbin=0; fbin<nr; fbin++) {
ff = f - (fbin + 1)*fshift;
if (ff >= 0) {
for(i=0; i<isize; i++) {
d2 = distance2(sx[f][i],sx[ff][i]);
bin = (int)(sqrt(d2)*invbin);
if (bin >= nalloc) {
nallocn = 10*(bin/10) + 11;
for(m=0; m<nr; m++) {
srenew(pr[m],nallocn);
for(i=nalloc; i<nallocn; i++)
pr[m][i] = 0;
}
nalloc = nallocn;
}
pr[fbin][bin]++;
}
rcount[fbin]++;
}
}
}
}
fprintf(stderr,"\n");
if (matfile) {
matmax = 0;
for(f=0; f<mat_nx; f++) {
normfac = 1.0/(mcount[f]*isize*rbin);
for(i=0; i<nbin; i++) {
mat[f][i] *= normfac;
if (mat[f][i] > matmax && (f!=0 || i!=0))
matmax = mat[f][i];
}
}
fprintf(stdout,"Value at (0,0): %.3f, maximum of the rest %.3f\n",
mat[0][0],matmax);
if (mmax > 0)
matmax = mmax;
snew(tickx,mat_nx);
for(f=0; f<mat_nx; f++) {
if (sbin == 0)
tickx[f] = f*dt;
else
tickx[f] = f*sbin;
}
snew(ticky,nbin+1);
for(i=0; i<=nbin; i++)
ticky[i] = i*rbin;
fp = ffopen(matfile,"w");
write_xpm(fp,MAT_SPATIAL_Y,"Van Hove function","G (1/nm)",
sbin==0 ? "time (ps)" : "sqrt(time) (ps^1/2)","r (nm)",
mat_nx,nbin,tickx,ticky,mat,0,matmax,rlo,rhi,&nlev);
ffclose(fp);
}
if (orfile) {
fp = xvgropen(orfile,"Van Hove function","r (nm)","G (nm\\S-1\\N)",oenv);
fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
snew(legend,nr);
for(fbin=0; fbin<nr; fbin++) {
sprintf(buf,"%g ps",(fbin + 1)*fshift*dt);
legend[fbin] = strdup(buf);
}
xvgr_legend(fp,nr,(const char**)legend,oenv);
for(i=0; i<nalloc; i++) {
fprintf(fp,"%g",i*rbin);
for(fbin=0; fbin<nr; fbin++)
fprintf(fp," %g",
(real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i==0 ? 0.5 : 1)));
fprintf(fp,"\n");
}
ffclose(fp);
}
if (otfile) {
sprintf(buf,"Probability of moving less than %g nm",rint);
fp = xvgropen(otfile,buf,"t (ps)","",oenv);
fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
for(f=0; f<=ftmax; f++)
fprintf(fp,"%g %g\n",f*dt,(real)pt[f]/(tcount[f]*isize));
ffclose(fp);
}
do_view(oenv, matfile,NULL);
do_view(oenv, orfile,NULL);
do_view(oenv, otfile,NULL);
thanx(stderr);
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_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;
}
