static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **r,
int ePBC, matrix box,
gmx_atomprop_t aps, real r_distance, int *atoms_added,
int *residues_added, real rshell, int max_sol,
const output_env_t oenv)
{
int i, nmol;
ivec n_box;
char filename[STRLEN];
char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt, *v_solvt = NULL;
real *r_solvt;
int ePBC_solvt;
matrix box_solvt;
int onr, onres;
char *lfn;
lfn = gmxlibfn(fn);
strncpy(filename, lfn, STRLEN);
sfree(lfn);
snew(atoms_solvt, 1);
get_stx_coordnum(filename, &(atoms_solvt->nr));
if (atoms_solvt->nr == 0)
{
gmx_fatal(FARGS, "No solvent in %s, please check your input\n", filename);
}
snew(x_solvt, atoms_solvt->nr);
if (v)
{
snew(v_solvt, atoms_solvt->nr);
}
snew(r_solvt, atoms_solvt->nr);
snew(atoms_solvt->resinfo, atoms_solvt->nr);
snew(atoms_solvt->atomname, atoms_solvt->nr);
snew(atoms_solvt->atom, atoms_solvt->nr);
atoms_solvt->pdbinfo = NULL;
fprintf(stderr, "Reading solvent configuration%s\n",
v_solvt ? " and velocities" : "");
read_stx_conf(filename, title_solvt, atoms_solvt, x_solvt, v_solvt,
&ePBC_solvt, box_solvt);
fprintf(stderr, "\"%s\"\n", title_solvt);
fprintf(stderr, "solvent configuration contains %d atoms in %d residues\n",
atoms_solvt->nr, atoms_solvt->nres);
fprintf(stderr, "\n");
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt, x_solvt, box_solvt);
/* initialise van der waals arrays of solvent configuration */
mk_vdw(atoms_solvt, r_solvt, aps, r_distance);
/* calculate the box multiplication factors n_box[0...DIM] */
nmol = 1;
for (i = 0; (i < DIM); i++)
{
n_box[i] = 1;
while (n_box[i]*box_solvt[i][i] < box[i][i])
{
n_box[i]++;
}
nmol *= n_box[i];
}
fprintf(stderr, "Will generate new solvent configuration of %dx%dx%d boxes\n",
n_box[XX], n_box[YY], n_box[ZZ]);
/* realloc atoms_solvt for the new solvent configuration */
srenew(atoms_solvt->resinfo, atoms_solvt->nres*nmol);
srenew(atoms_solvt->atomname, atoms_solvt->nr*nmol);
srenew(atoms_solvt->atom, atoms_solvt->nr*nmol);
srenew(x_solvt, atoms_solvt->nr*nmol);
if (v_solvt)
{
srenew(v_solvt, atoms_solvt->nr*nmol);
}
srenew(r_solvt, atoms_solvt->nr*nmol);
/* generate a new solvent configuration */
genconf(atoms_solvt, x_solvt, v_solvt, r_solvt, box_solvt, n_box);
#ifdef DEBUG
print_stat(x_solvt, atoms_solvt->nr, box_solvt);
#endif
#ifdef DEBUG
print_stat(x_solvt, atoms_solvt->nr, box_solvt);
#endif
/* Sort the solvent mixture, not the protein... */
sort_molecule(&atoms_solvt, x_solvt, v_solvt, r_solvt);
/* add the two configurations */
onr = atoms->nr;
onres = atoms->nres;
add_conf(atoms, x, v, r, TRUE, ePBC, box, FALSE,
atoms_solvt, x_solvt, v_solvt, r_solvt, TRUE, rshell, max_sol, oenv);
*atoms_added = atoms->nr-onr;
*residues_added = atoms->nres-onres;
sfree(x_solvt);
sfree(r_solvt);
fprintf(stderr, "Generated solvent containing %d atoms in %d residues\n",
*atoms_added, *residues_added);
}
static char *insert_mols(char *mol_insrt,int nmol_insrt,int ntry,int seed,
t_atoms *atoms,rvec **x,real **r,int ePBC,matrix box,
gmx_atomprop_t aps,real r_distance,real rshell)
{
t_pbc pbc;
static char *title_insrt;
t_atoms atoms_insrt;
rvec *x_insrt,*x_n;
real *r_insrt;
int ePBC_insrt;
matrix box_insrt;
int i,mol,onr;
real alfa,beta,gamma;
rvec offset_x;
int try;
set_pbc(&pbc,ePBC,box);
/* read number of atoms of insert molecules */
get_stx_coordnum(mol_insrt,&atoms_insrt.nr);
if (atoms_insrt.nr == 0)
gmx_fatal(FARGS,"No molecule in %s, please check your input\n",mol_insrt);
/* allocate memory for atom coordinates of insert molecules */
snew(x_insrt,atoms_insrt.nr);
snew(r_insrt,atoms_insrt.nr);
snew(atoms_insrt.resname,atoms_insrt.nr);
snew(atoms_insrt.atomname,atoms_insrt.nr);
snew(atoms_insrt.atom,atoms_insrt.nr);
atoms_insrt.pdbinfo = NULL;
snew(x_n,atoms_insrt.nr);
snew(title_insrt,STRLEN);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr,"Reading molecule configuration \n");
read_stx_conf(mol_insrt,title_insrt,&atoms_insrt,x_insrt,NULL,
&ePBC_insrt,box_insrt);
fprintf(stderr,"%s\nContaining %d atoms in %d residue\n",
title_insrt,atoms_insrt.nr,atoms_insrt.nres);
srenew(atoms_insrt.resname,atoms_insrt.nres);
/* initialise van der waals arrays of insert molecules */
mk_vdw(&atoms_insrt,r_insrt,aps,r_distance);
srenew(atoms->resname,(atoms->nres+nmol_insrt));
srenew(atoms->atomname,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(atoms->atom,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*x,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*r,(atoms->nr+atoms_insrt.nr*nmol_insrt));
try=mol=0;
while ((mol < nmol_insrt) && (try < ntry*nmol_insrt)) {
fprintf(stderr,"\rTry %d",try++);
for (i=0;(i<atoms_insrt.nr);i++) {
if (atoms_insrt.atom[i].resnr!=0)
gmx_fatal(FARGS,"more then one residue in insert molecules\n"
"program terminated\n");
copy_rvec(x_insrt[i],x_n[i]);
}
alfa=2*M_PI*rando(&seed);
beta=2*M_PI*rando(&seed);
gamma=2*M_PI*rando(&seed);
rotate_conf(atoms_insrt.nr,x_n,NULL,alfa,beta,gamma);
offset_x[XX]=box[XX][XX]*rando(&seed);
offset_x[YY]=box[YY][YY]*rando(&seed);
offset_x[ZZ]=box[ZZ][ZZ]*rando(&seed);
gen_box(0,atoms_insrt.nr,x_n,box_insrt,offset_x,TRUE);
if (!in_box(&pbc,x_n[0]) || !in_box(&pbc,x_n[atoms_insrt.nr-1]))
continue;
onr=atoms->nr;
add_conf(atoms,x,NULL,r,FALSE,ePBC,box,TRUE,
&atoms_insrt,x_n,NULL,r_insrt,FALSE,rshell,0);
if (atoms->nr==(atoms_insrt.nr+onr)) {
mol++;
fprintf(stderr," success (now %d atoms)!",atoms->nr);
}
}
srenew(atoms->resname, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
srenew(*r, atoms->nr);
fprintf(stderr,"\n");
/* print number of molecules added */
fprintf(stderr,"Added %d molecules (out of %d requested) of %s\n",
mol,nmol_insrt,*atoms_insrt.resname[0]);
return title_insrt;
}
static void add_solv(char *fn,t_atoms *atoms,rvec **x,rvec **v,real **r,
int ePBC,matrix box,
gmx_atomprop_t aps,real r_distance,int *atoms_added,
int *residues_added,real rshell,int max_sol)
{
int i,nmol;
ivec n_box;
char filename[STRLEN];
char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt,*v_solvt=NULL;
real *r_solvt;
int ePBC_solvt;
matrix box_solvt;
int onr,onres;
strncpy(filename,libfn(fn),STRLEN);
snew(atoms_solvt,1);
get_stx_coordnum(filename,&(atoms_solvt->nr));
if (atoms_solvt->nr == 0)
gmx_fatal(FARGS,"No solvent in %s, please check your input\n",filename);
snew(x_solvt,atoms_solvt->nr);
if (v) snew(v_solvt,atoms_solvt->nr);
snew(r_solvt,atoms_solvt->nr);
snew(atoms_solvt->resname,atoms_solvt->nr);
snew(atoms_solvt->atomname,atoms_solvt->nr);
snew(atoms_solvt->atom,atoms_solvt->nr);
atoms_solvt->pdbinfo = NULL;
fprintf(stderr,"Reading solvent configuration%s\n",
v_solvt?" and velocities":"");
read_stx_conf(filename,title_solvt,atoms_solvt,x_solvt,v_solvt,
&ePBC_solvt,box_solvt);
fprintf(stderr,"\"%s\"\n",title_solvt);
fprintf(stderr,"solvent configuration contains %d atoms in %d residues\n",
atoms_solvt->nr,atoms_solvt->nres);
fprintf(stderr,"\n");
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt,x_solvt,box_solvt);
/* initialise van der waals arrays of solvent configuration */
mk_vdw(atoms_solvt,r_solvt,aps,r_distance);
/* calculate the box multiplication factors n_box[0...DIM] */
nmol=1;
for (i=0; (i < DIM);i++) {
n_box[i] = 1;
while (n_box[i]*box_solvt[i][i] < box[i][i])
n_box[i]++;
nmol*=n_box[i];
}
fprintf(stderr,"Will generate new solvent configuration of %dx%dx%d boxes\n",
n_box[XX],n_box[YY],n_box[ZZ]);
/* realloc atoms_solvt for the new solvent configuration */
srenew(atoms_solvt->resname,atoms_solvt->nres*nmol);
srenew(atoms_solvt->atomname,atoms_solvt->nr*nmol);
srenew(atoms_solvt->atom,atoms_solvt->nr*nmol);
srenew(x_solvt,atoms_solvt->nr*nmol);
if (v_solvt) srenew(v_solvt,atoms_solvt->nr*nmol);
srenew(r_solvt,atoms_solvt->nr*nmol);
/* generate a new solvent configuration */
genconf(atoms_solvt,x_solvt,v_solvt,r_solvt,box_solvt,n_box);
#ifdef DEBUG
print_stat(x_solvt,atoms_solvt->nr,box_solvt);
#endif
#ifdef DEBUG
print_stat(x_solvt,atoms_solvt->nr,box_solvt);
#endif
/* Sort the solvent mixture, not the protein... */
sort_molecule(&atoms_solvt,x_solvt,v_solvt,r_solvt);
/* add the two configurations */
onr=atoms->nr;
onres=atoms->nres;
add_conf(atoms,x,v,r,TRUE,ePBC,box,FALSE,
atoms_solvt,x_solvt,v_solvt,r_solvt,TRUE,rshell,max_sol);
*atoms_added=atoms->nr-onr;
*residues_added=atoms->nres-onres;
sfree(x_solvt);
sfree(r_solvt);
fprintf(stderr,"Generated solvent containing %d atoms in %d residues\n",
*atoms_added,*residues_added);
}
static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
gmx_atomprop_t aps, real r_distance, real rshell,
const output_env_t oenv)
{
t_pbc pbc;
static char *title_insrt;
t_atoms atoms_insrt;
rvec *x_insrt, *x_n;
real *r_insrt;
int ePBC_insrt;
matrix box_insrt;
int i, mol, onr;
real alfa, beta, gamma;
rvec offset_x;
int trial;
set_pbc(&pbc, ePBC, box);
/* read number of atoms of insert molecules */
get_stx_coordnum(mol_insrt, &atoms_insrt.nr);
if (atoms_insrt.nr == 0)
{
gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
}
/* allocate memory for atom coordinates of insert molecules */
snew(x_insrt, atoms_insrt.nr);
snew(r_insrt, atoms_insrt.nr);
snew(atoms_insrt.resinfo, atoms_insrt.nr);
snew(atoms_insrt.atomname, atoms_insrt.nr);
snew(atoms_insrt.atom, atoms_insrt.nr);
atoms_insrt.pdbinfo = NULL;
snew(x_n, atoms_insrt.nr);
snew(title_insrt, STRLEN);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr, "Reading molecule configuration \n");
read_stx_conf(mol_insrt, title_insrt, &atoms_insrt, x_insrt, NULL,
&ePBC_insrt, box_insrt);
fprintf(stderr, "%s\nContaining %d atoms in %d residue\n",
title_insrt, atoms_insrt.nr, atoms_insrt.nres);
srenew(atoms_insrt.resinfo, atoms_insrt.nres);
/* initialise van der waals arrays of insert molecules */
mk_vdw(&atoms_insrt, r_insrt, aps, r_distance);
srenew(atoms->resinfo, (atoms->nres+nmol_insrt*atoms_insrt.nres));
srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*r, (atoms->nr+atoms_insrt.nr*nmol_insrt));
trial = mol = 0;
while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
{
fprintf(stderr, "\rTry %d", trial++);
for (i = 0; (i < atoms_insrt.nr); i++)
{
copy_rvec(x_insrt[i], x_n[i]);
}
alfa = 2*M_PI*rando( &seed);
beta = 2*M_PI*rando( &seed);
gamma = 2*M_PI*rando( &seed);
rotate_conf(atoms_insrt.nr, x_n, NULL, alfa, beta, gamma);
offset_x[XX] = box[XX][XX]*rando(&seed);
offset_x[YY] = box[YY][YY]*rando(&seed);
offset_x[ZZ] = box[ZZ][ZZ]*rando(&seed);
gen_box(0, atoms_insrt.nr, x_n, box_insrt, offset_x, TRUE);
if (!in_box(&pbc, x_n[0]) || !in_box(&pbc, x_n[atoms_insrt.nr-1]))
{
continue;
}
onr = atoms->nr;
add_conf(atoms, x, NULL, r, FALSE, ePBC, box, TRUE,
&atoms_insrt, x_n, NULL, r_insrt, FALSE, rshell, 0, oenv);
if (atoms->nr == (atoms_insrt.nr+onr))
{
mol++;
fprintf(stderr, " success (now %d atoms)!", atoms->nr);
}
}
srenew(atoms->resinfo, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
srenew(*r, atoms->nr);
fprintf(stderr, "\n");
/* print number of molecules added */
fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
return title_insrt;
}
static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
gmx_atomprop_t aps,
real r_distance, real r_scale, real rshell,
const output_env_t oenv,
const char* posfn, const rvec deltaR, int enum_rot,
gmx_bool bCheckAllPairDist)
{
t_pbc pbc;
static char *title_insrt;
t_atoms atoms_insrt;
rvec *x_insrt, *x_n;
real *r_insrt;
int ePBC_insrt;
matrix box_insrt;
int i, mol, onr, ncol;
real alfa = 0., beta = 0., gamma = 0.;
rvec offset_x;
int trial;
double **rpos;
set_pbc(&pbc, ePBC, box);
/* read number of atoms of insert molecules */
get_stx_coordnum(mol_insrt, &atoms_insrt.nr);
if (atoms_insrt.nr == 0)
{
gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
}
/* allocate memory for atom coordinates of insert molecules */
snew(x_insrt, atoms_insrt.nr);
snew(r_insrt, atoms_insrt.nr);
snew(atoms_insrt.resinfo, atoms_insrt.nr);
snew(atoms_insrt.atomname, atoms_insrt.nr);
snew(atoms_insrt.atom, atoms_insrt.nr);
atoms_insrt.pdbinfo = NULL;
snew(x_n, atoms_insrt.nr);
snew(title_insrt, STRLEN);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr, "Reading molecule configuration \n");
read_stx_conf(mol_insrt, title_insrt, &atoms_insrt, x_insrt, NULL,
&ePBC_insrt, box_insrt);
fprintf(stderr, "%s\nContaining %d atoms in %d residue\n",
title_insrt, atoms_insrt.nr, atoms_insrt.nres);
srenew(atoms_insrt.resinfo, atoms_insrt.nres);
/* initialise van der waals arrays of insert molecules */
mk_vdw(&atoms_insrt, r_insrt, aps, r_distance, r_scale);
/* With -ip, take nmol_insrt from file posfn */
if (posfn != NULL)
{
nmol_insrt = read_xvg(posfn, &rpos, &ncol);
if (ncol != 3)
{
gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n", ncol, posfn);
}
fprintf(stderr, "Read %d positions from file %s\n\n", nmol_insrt, posfn);
}
srenew(atoms->resinfo, (atoms->nres+nmol_insrt*atoms_insrt.nres));
srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*r, (atoms->nr+atoms_insrt.nr*nmol_insrt));
trial = mol = 0;
while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
{
fprintf(stderr, "\rTry %d", trial++);
for (i = 0; (i < atoms_insrt.nr); i++)
{
copy_rvec(x_insrt[i], x_n[i]);
}
switch (enum_rot)
{
case en_rotXYZ:
alfa = 2*M_PI *rando(&seed);
beta = 2*M_PI *rando(&seed);
gamma = 2*M_PI *rando(&seed);
break;
case en_rotZ:
alfa = beta = 0.;
gamma = 2*M_PI*rando(&seed);
break;
case en_rotNone:
alfa = beta = gamma = 0.;
break;
}
if (enum_rot == en_rotXYZ || (enum_rot == en_rotZ))
{
rotate_conf(atoms_insrt.nr, x_n, NULL, alfa, beta, gamma);
}
if (posfn == NULL)
{
/* insert at random positions */
offset_x[XX] = box[XX][XX]*rando(&seed);
offset_x[YY] = box[YY][YY]*rando(&seed);
offset_x[ZZ] = box[ZZ][ZZ]*rando(&seed);
gen_box(0, atoms_insrt.nr, x_n, box_insrt, offset_x, TRUE);
if (!in_box(&pbc, x_n[0]) || !in_box(&pbc, x_n[atoms_insrt.nr-1]))
{
continue;
}
}
else
{
/* Insert at positions taken from option -ip file */
offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2*rando(&seed)-1);
offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2*rando(&seed)-1);
offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2*rando(&seed)-1);
for (i = 0; i < atoms_insrt.nr; i++)
{
rvec_inc(x_n[i], offset_x);
}
}
onr = atoms->nr;
/* This is a (maybe) slow workaround to avoid too many calls of add_conf, which
* leaks memory (status May 2012). If the momory leaks in add_conf() are fixed,
* this check could be removed. Note, however, that allPairsDistOk is probably
* even faster than add_conf() when inserting a small molecule into a moderately
* small system.
*/
if (bCheckAllPairDist && !allPairsDistOk(atoms, *x, *r, ePBC, box, &atoms_insrt, x_n, r_insrt))
{
continue;
}
add_conf(atoms, x, NULL, r, FALSE, ePBC, box, TRUE,
&atoms_insrt, x_n, NULL, r_insrt, FALSE, rshell, 0, oenv);
if (atoms->nr == (atoms_insrt.nr+onr))
{
mol++;
fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
}
}
srenew(atoms->resinfo, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
srenew(*r, atoms->nr);
fprintf(stderr, "\n");
/* print number of molecules added */
fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
return title_insrt;
}
