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47 #include <sys/types.h>
49 #include "gromacs/commandline/pargs.h"
50 #include "gromacs/fileio/confio.h"
51 #include "gromacs/fileio/enxio.h"
52 #include "gromacs/fileio/gmxfio.h"
53 #include "gromacs/fileio/tpxio.h"
54 #include "gromacs/fileio/trnio.h"
55 #include "gromacs/fileio/trxio.h"
56 #include "gromacs/gmxpreprocess/add_par.h"
57 #include "gromacs/gmxpreprocess/calc_verletbuf.h"
58 #include "gromacs/gmxpreprocess/compute_io.h"
59 #include "gromacs/gmxpreprocess/convparm.h"
60 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
61 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
62 #include "gromacs/gmxpreprocess/grompp-impl.h"
63 #include "gromacs/gmxpreprocess/readir.h"
64 #include "gromacs/gmxpreprocess/sortwater.h"
65 #include "gromacs/gmxpreprocess/tomorse.h"
66 #include "gromacs/gmxpreprocess/topio.h"
67 #include "gromacs/gmxpreprocess/toputil.h"
68 #include "gromacs/gmxpreprocess/vsite_parm.h"
69 #include "gromacs/imd/imd.h"
70 #include "gromacs/legacyheaders/calcgrid.h"
71 #include "gromacs/legacyheaders/genborn.h"
72 #include "gromacs/legacyheaders/macros.h"
73 #include "gromacs/legacyheaders/names.h"
74 #include "gromacs/legacyheaders/perf_est.h"
75 #include "gromacs/legacyheaders/splitter.h"
76 #include "gromacs/legacyheaders/txtdump.h"
77 #include "gromacs/legacyheaders/warninp.h"
78 #include "gromacs/math/vec.h"
79 #include "gromacs/pbcutil/pbc.h"
80 #include "gromacs/random/random.h"
81 #include "gromacs/topology/mtop_util.h"
82 #include "gromacs/topology/symtab.h"
83 #include "gromacs/topology/topology.h"
84 #include "gromacs/utility/cstringutil.h"
85 #include "gromacs/utility/fatalerror.h"
86 #include "gromacs/utility/futil.h"
87 #include "gromacs/utility/smalloc.h"
88 #include "gromacs/utility/snprintf.h"
90 static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
95 /* For all the molecule types */
96 for (i = 0; i < nrmols; i++)
98 n += mols[i].plist[ifunc].nr;
99 mols[i].plist[ifunc].nr = 0;
104 static int check_atom_names(const char *fn1, const char *fn2,
105 gmx_mtop_t *mtop, t_atoms *at)
107 int mb, m, i, j, nmismatch;
109 #define MAXMISMATCH 20
111 if (mtop->natoms != at->nr)
113 gmx_incons("comparing atom names");
118 for (mb = 0; mb < mtop->nmolblock; mb++)
120 tat = &mtop->moltype[mtop->molblock[mb].type].atoms;
121 for (m = 0; m < mtop->molblock[mb].nmol; m++)
123 for (j = 0; j < tat->nr; j++)
125 if (strcmp( *(tat->atomname[j]), *(at->atomname[i]) ) != 0)
127 if (nmismatch < MAXMISMATCH)
130 "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
131 i+1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
133 else if (nmismatch == MAXMISMATCH)
135 fprintf(stderr, "(more than %d non-matching atom names)\n", MAXMISMATCH);
147 static void check_eg_vs_cg(gmx_mtop_t *mtop)
149 int astart, mb, m, cg, j, firstj;
150 unsigned char firsteg, eg;
153 /* Go through all the charge groups and make sure all their
154 * atoms are in the same energy group.
158 for (mb = 0; mb < mtop->nmolblock; mb++)
160 molt = &mtop->moltype[mtop->molblock[mb].type];
161 for (m = 0; m < mtop->molblock[mb].nmol; m++)
163 for (cg = 0; cg < molt->cgs.nr; cg++)
165 /* Get the energy group of the first atom in this charge group */
166 firstj = astart + molt->cgs.index[cg];
167 firsteg = ggrpnr(&mtop->groups, egcENER, firstj);
168 for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
170 eg = ggrpnr(&mtop->groups, egcENER, astart+j);
173 gmx_fatal(FARGS, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
174 firstj+1, astart+j+1, cg+1, *molt->name);
178 astart += molt->atoms.nr;
183 static void check_cg_sizes(const char *topfn, t_block *cgs, warninp_t wi)
186 char warn_buf[STRLEN];
189 for (cg = 0; cg < cgs->nr; cg++)
191 maxsize = max(maxsize, cgs->index[cg+1]-cgs->index[cg]);
194 if (maxsize > MAX_CHARGEGROUP_SIZE)
196 gmx_fatal(FARGS, "The largest charge group contains %d atoms. The maximum is %d.", maxsize, MAX_CHARGEGROUP_SIZE);
198 else if (maxsize > 10)
200 set_warning_line(wi, topfn, -1);
202 "The largest charge group contains %d atoms.\n"
203 "Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.\n"
204 "For efficiency and accuracy, charge group should consist of a few atoms.\n"
205 "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
207 warning_note(wi, warn_buf);
211 static void check_bonds_timestep(gmx_mtop_t *mtop, double dt, warninp_t wi)
213 /* This check is not intended to ensure accurate integration,
214 * rather it is to signal mistakes in the mdp settings.
215 * A common mistake is to forget to turn on constraints
216 * for MD after energy minimization with flexible bonds.
217 * This check can also detect too large time steps for flexible water
218 * models, but such errors will often be masked by the constraints
219 * mdp options, which turns flexible water into water with bond constraints,
220 * but without an angle constraint. Unfortunately such incorrect use
221 * of water models can not easily be detected without checking
222 * for specific model names.
224 * The stability limit of leap-frog or velocity verlet is 4.44 steps
225 * per oscillational period.
226 * But accurate bonds distributions are lost far before that limit.
227 * To allow relatively common schemes (although not common with Gromacs)
228 * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
229 * we set the note limit to 10.
231 int min_steps_warn = 5;
232 int min_steps_note = 10;
235 gmx_moltype_t *moltype, *w_moltype;
237 t_ilist *ilist, *ilb, *ilc, *ils;
239 int i, a1, a2, w_a1, w_a2, j;
240 real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
241 gmx_bool bFound, bWater, bWarn;
242 char warn_buf[STRLEN];
244 ip = mtop->ffparams.iparams;
246 twopi2 = sqr(2*M_PI);
248 limit2 = sqr(min_steps_note*dt);
254 for (molt = 0; molt < mtop->nmoltype; molt++)
256 moltype = &mtop->moltype[molt];
257 atom = moltype->atoms.atom;
258 ilist = moltype->ilist;
259 ilc = &ilist[F_CONSTR];
260 ils = &ilist[F_SETTLE];
261 for (ftype = 0; ftype < F_NRE; ftype++)
263 if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
269 for (i = 0; i < ilb->nr; i += 3)
271 fc = ip[ilb->iatoms[i]].harmonic.krA;
272 re = ip[ilb->iatoms[i]].harmonic.rA;
273 if (ftype == F_G96BONDS)
275 /* Convert squared sqaure fc to harmonic fc */
278 a1 = ilb->iatoms[i+1];
279 a2 = ilb->iatoms[i+2];
282 if (fc > 0 && m1 > 0 && m2 > 0)
284 period2 = twopi2*m1*m2/((m1 + m2)*fc);
288 period2 = GMX_FLOAT_MAX;
292 fprintf(debug, "fc %g m1 %g m2 %g period %g\n",
293 fc, m1, m2, sqrt(period2));
295 if (period2 < limit2)
298 for (j = 0; j < ilc->nr; j += 3)
300 if ((ilc->iatoms[j+1] == a1 && ilc->iatoms[j+2] == a2) ||
301 (ilc->iatoms[j+1] == a2 && ilc->iatoms[j+2] == a1))
306 for (j = 0; j < ils->nr; j += 4)
308 if ((a1 == ils->iatoms[j+1] || a1 == ils->iatoms[j+2] || a1 == ils->iatoms[j+3]) &&
309 (a2 == ils->iatoms[j+1] || a2 == ils->iatoms[j+2] || a2 == ils->iatoms[j+3]))
315 (w_moltype == NULL || period2 < w_period2))
327 if (w_moltype != NULL)
329 bWarn = (w_period2 < sqr(min_steps_warn*dt));
330 /* A check that would recognize most water models */
331 bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
332 w_moltype->atoms.nr <= 5);
333 sprintf(warn_buf, "The bond in molecule-type %s between atoms %d %s and %d %s has an estimated oscillational period of %.1e ps, which is less than %d times the time step of %.1e ps.\n"
336 w_a1+1, *w_moltype->atoms.atomname[w_a1],
337 w_a2+1, *w_moltype->atoms.atomname[w_a2],
338 sqrt(w_period2), bWarn ? min_steps_warn : min_steps_note, dt,
340 "Maybe you asked for fexible water." :
341 "Maybe you forgot to change the constraints mdp option.");
344 warning(wi, warn_buf);
348 warning_note(wi, warn_buf);
353 static void check_vel(gmx_mtop_t *mtop, rvec v[])
355 gmx_mtop_atomloop_all_t aloop;
359 aloop = gmx_mtop_atomloop_all_init(mtop);
360 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
362 if (atom->ptype == eptShell ||
363 atom->ptype == eptBond ||
364 atom->ptype == eptVSite)
371 static void check_shells_inputrec(gmx_mtop_t *mtop,
375 gmx_mtop_atomloop_all_t aloop;
378 char warn_buf[STRLEN];
380 aloop = gmx_mtop_atomloop_all_init(mtop);
381 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
383 if (atom->ptype == eptShell ||
384 atom->ptype == eptBond)
389 if (IR_TWINRANGE(*ir) && (nshells > 0))
391 snprintf(warn_buf, STRLEN,
392 "The combination of using shells and a twin-range cut-off is not supported");
393 warning_error(wi, warn_buf);
395 if ((nshells > 0) && (ir->nstcalcenergy != 1))
397 set_warning_line(wi, "unknown", -1);
398 snprintf(warn_buf, STRLEN,
399 "There are %d shells, changing nstcalcenergy from %d to 1",
400 nshells, ir->nstcalcenergy);
401 ir->nstcalcenergy = 1;
402 warning(wi, warn_buf);
406 /* TODO Decide whether this function can be consolidated with
407 * gmx_mtop_ftype_count */
408 static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
413 for (mb = 0; mb < mtop->nmolblock; mb++)
415 nint += mtop->molblock[mb].nmol*mi[mtop->molblock[mb].type].plist[ftype].nr;
421 /* This routine reorders the molecule type array
422 * in the order of use in the molblocks,
423 * unused molecule types are deleted.
425 static void renumber_moltypes(gmx_mtop_t *sys,
426 int *nmolinfo, t_molinfo **molinfo)
428 int *order, norder, i;
432 snew(order, *nmolinfo);
434 for (mb = 0; mb < sys->nmolblock; mb++)
436 for (i = 0; i < norder; i++)
438 if (order[i] == sys->molblock[mb].type)
445 /* This type did not occur yet, add it */
446 order[norder] = sys->molblock[mb].type;
447 /* Renumber the moltype in the topology */
450 sys->molblock[mb].type = i;
453 /* We still need to reorder the molinfo structs */
455 for (mi = 0; mi < *nmolinfo; mi++)
457 for (i = 0; i < norder; i++)
466 done_mi(&(*molinfo)[mi]);
470 minew[i] = (*molinfo)[mi];
479 static void molinfo2mtop(int nmi, t_molinfo *mi, gmx_mtop_t *mtop)
484 mtop->nmoltype = nmi;
485 snew(mtop->moltype, nmi);
486 for (m = 0; m < nmi; m++)
488 molt = &mtop->moltype[m];
489 molt->name = mi[m].name;
490 molt->atoms = mi[m].atoms;
491 /* ilists are copied later */
492 molt->cgs = mi[m].cgs;
493 molt->excls = mi[m].excls;
498 new_status(const char *topfile, const char *topppfile, const char *confin,
499 t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero,
500 gmx_bool bGenVel, gmx_bool bVerbose, t_state *state,
501 gpp_atomtype_t atype, gmx_mtop_t *sys,
502 int *nmi, t_molinfo **mi, t_params plist[],
503 int *comb, double *reppow, real *fudgeQQ,
507 t_molinfo *molinfo = NULL;
509 gmx_molblock_t *molblock, *molbs;
511 int mb, i, nrmols, nmismatch;
513 gmx_bool bGB = FALSE;
514 char warn_buf[STRLEN];
518 /* Set gmx_boolean for GB */
519 if (ir->implicit_solvent)
524 /* TOPOLOGY processing */
525 sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
526 plist, comb, reppow, fudgeQQ,
527 atype, &nrmols, &molinfo, ir,
528 &nmolblock, &molblock, bGB,
532 snew(sys->molblock, nmolblock);
535 for (mb = 0; mb < nmolblock; mb++)
537 if (sys->nmolblock > 0 &&
538 molblock[mb].type == sys->molblock[sys->nmolblock-1].type)
540 /* Merge consecutive blocks with the same molecule type */
541 sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
542 sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
544 else if (molblock[mb].nmol > 0)
546 /* Add a new molblock to the topology */
547 molbs = &sys->molblock[sys->nmolblock];
548 *molbs = molblock[mb];
549 molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
550 molbs->nposres_xA = 0;
551 molbs->nposres_xB = 0;
552 sys->natoms += molbs->nmol*molbs->natoms_mol;
556 if (sys->nmolblock == 0)
558 gmx_fatal(FARGS, "No molecules were defined in the system");
561 renumber_moltypes(sys, &nrmols, &molinfo);
565 convert_harmonics(nrmols, molinfo, atype);
568 if (ir->eDisre == edrNone)
570 i = rm_interactions(F_DISRES, nrmols, molinfo);
573 set_warning_line(wi, "unknown", -1);
574 sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
575 warning_note(wi, warn_buf);
578 if (opts->bOrire == FALSE)
580 i = rm_interactions(F_ORIRES, nrmols, molinfo);
583 set_warning_line(wi, "unknown", -1);
584 sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
585 warning_note(wi, warn_buf);
589 /* Copy structures from msys to sys */
590 molinfo2mtop(nrmols, molinfo, sys);
592 gmx_mtop_finalize(sys);
594 /* COORDINATE file processing */
597 fprintf(stderr, "processing coordinates...\n");
600 get_stx_coordnum(confin, &state->natoms);
601 if (state->natoms != sys->natoms)
603 gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
604 " does not match topology (%s, %d)",
605 confin, state->natoms, topfile, sys->natoms);
609 /* make space for coordinates and velocities */
612 init_t_atoms(confat, state->natoms, FALSE);
613 init_state(state, state->natoms, 0, 0, 0, 0);
614 read_stx_conf(confin, title, confat, state->x, state->v, NULL, state->box);
615 /* This call fixes the box shape for runs with pressure scaling */
616 set_box_rel(ir, state);
618 nmismatch = check_atom_names(topfile, confin, sys, confat);
619 free_t_atoms(confat, TRUE);
624 sprintf(buf, "%d non-matching atom name%s\n"
625 "atom names from %s will be used\n"
626 "atom names from %s will be ignored\n",
627 nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
631 /* Do more checks, mostly related to constraints */
634 fprintf(stderr, "double-checking input for internal consistency...\n");
637 int bHasNormalConstraints = 0 < (nint_ftype(sys, molinfo, F_CONSTR) +
638 nint_ftype(sys, molinfo, F_CONSTRNC));
639 int bHasAnyConstraints = bHasNormalConstraints || 0 < nint_ftype(sys, molinfo, F_SETTLE);
640 double_check(ir, state->box,
641 bHasNormalConstraints,
650 gmx_mtop_atomloop_all_t aloop;
654 snew(mass, state->natoms);
655 aloop = gmx_mtop_atomloop_all_init(sys);
656 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
662 if (opts->seed == -1)
664 useed = (int)gmx_rng_make_seed();
665 fprintf(stderr, "Setting gen_seed to %u\n", useed);
667 maxwell_speed(opts->tempi, useed, sys, state->v);
669 stop_cm(stdout, state->natoms, mass, state->x, state->v);
677 static void copy_state(const char *slog, t_trxframe *fr,
678 gmx_bool bReadVel, t_state *state,
683 if (fr->not_ok & FRAME_NOT_OK)
685 gmx_fatal(FARGS, "Can not start from an incomplete frame");
689 gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s",
693 for (i = 0; i < state->natoms; i++)
695 copy_rvec(fr->x[i], state->x[i]);
701 gmx_incons("Trajecory frame unexpectedly does not contain velocities");
703 for (i = 0; i < state->natoms; i++)
705 copy_rvec(fr->v[i], state->v[i]);
710 copy_mat(fr->box, state->box);
713 *use_time = fr->time;
716 static void cont_status(const char *slog, const char *ener,
717 gmx_bool bNeedVel, gmx_bool bGenVel, real fr_time,
718 t_inputrec *ir, t_state *state,
720 const output_env_t oenv)
721 /* If fr_time == -1 read the last frame available which is complete */
729 bReadVel = (bNeedVel && !bGenVel);
732 "Reading Coordinates%s and Box size from old trajectory\n",
733 bReadVel ? ", Velocities" : "");
736 fprintf(stderr, "Will read whole trajectory\n");
740 fprintf(stderr, "Will read till time %g\n", fr_time);
746 fprintf(stderr, "Velocities generated: "
747 "ignoring velocities in input trajectory\n");
749 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
753 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X | TRX_NEED_V);
759 "WARNING: Did not find a frame with velocities in file %s,\n"
760 " all velocities will be set to zero!\n\n", slog);
761 for (i = 0; i < sys->natoms; i++)
763 clear_rvec(state->v[i]);
766 /* Search for a frame without velocities */
768 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
772 state->natoms = fr.natoms;
774 if (sys->natoms != state->natoms)
776 gmx_fatal(FARGS, "Number of atoms in Topology "
777 "is not the same as in Trajectory");
779 copy_state(slog, &fr, bReadVel, state, &use_time);
781 /* Find the appropriate frame */
782 while ((fr_time == -1 || fr.time < fr_time) &&
783 read_next_frame(oenv, fp, &fr))
785 copy_state(slog, &fr, bReadVel, state, &use_time);
790 /* Set the relative box lengths for preserving the box shape.
791 * Note that this call can lead to differences in the last bit
792 * with respect to using gmx convert-tpr to create a [REF].tpx[ref] file.
794 set_box_rel(ir, state);
796 fprintf(stderr, "Using frame at t = %g ps\n", use_time);
797 fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
799 if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
801 get_enx_state(ener, use_time, &sys->groups, ir, state);
802 preserve_box_shape(ir, state->box_rel, state->boxv);
806 static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
808 int rc_scaling, int ePBC,
812 gmx_bool bFirst = TRUE, *hadAtom;
818 int natoms, npbcdim = 0;
819 char warn_buf[STRLEN], title[STRLEN];
820 int a, i, ai, j, k, mb, nat_molb;
821 gmx_molblock_t *molb;
825 get_stx_coordnum(fn, &natoms);
826 if (natoms != mtop->natoms)
828 sprintf(warn_buf, "The number of atoms in %s (%d) does not match the number of atoms in the topology (%d). Will assume that the first %d atoms in the topology and %s match.", fn, natoms, mtop->natoms, min(mtop->natoms, natoms), fn);
829 warning(wi, warn_buf);
833 init_t_atoms(&dumat, natoms, FALSE);
834 read_stx_conf(fn, title, &dumat, x, v, NULL, box);
836 npbcdim = ePBC2npbcdim(ePBC);
838 if (rc_scaling != erscNO)
840 copy_mat(box, invbox);
841 for (j = npbcdim; j < DIM; j++)
843 clear_rvec(invbox[j]);
846 m_inv_ur0(invbox, invbox);
849 /* Copy the reference coordinates to mtop */
853 snew(hadAtom, natoms);
854 for (mb = 0; mb < mtop->nmolblock; mb++)
856 molb = &mtop->molblock[mb];
857 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
858 pr = &(molinfo[molb->type].plist[F_POSRES]);
859 prfb = &(molinfo[molb->type].plist[F_FBPOSRES]);
860 if (pr->nr > 0 || prfb->nr > 0)
862 atom = mtop->moltype[molb->type].atoms.atom;
863 for (i = 0; (i < pr->nr); i++)
865 ai = pr->param[i].AI;
868 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
869 ai+1, *molinfo[molb->type].name, fn, natoms);
872 if (rc_scaling == erscCOM)
874 /* Determine the center of mass of the posres reference coordinates */
875 for (j = 0; j < npbcdim; j++)
877 sum[j] += atom[ai].m*x[a+ai][j];
879 totmass += atom[ai].m;
882 /* Same for flat-bottomed posres, but do not count an atom twice for COM */
883 for (i = 0; (i < prfb->nr); i++)
885 ai = prfb->param[i].AI;
888 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
889 ai+1, *molinfo[molb->type].name, fn, natoms);
891 if (rc_scaling == erscCOM && hadAtom[ai] == FALSE)
893 /* Determine the center of mass of the posres reference coordinates */
894 for (j = 0; j < npbcdim; j++)
896 sum[j] += atom[ai].m*x[a+ai][j];
898 totmass += atom[ai].m;
903 molb->nposres_xA = nat_molb;
904 snew(molb->posres_xA, molb->nposres_xA);
905 for (i = 0; i < nat_molb; i++)
907 copy_rvec(x[a+i], molb->posres_xA[i]);
912 molb->nposres_xB = nat_molb;
913 snew(molb->posres_xB, molb->nposres_xB);
914 for (i = 0; i < nat_molb; i++)
916 copy_rvec(x[a+i], molb->posres_xB[i]);
922 if (rc_scaling == erscCOM)
926 gmx_fatal(FARGS, "The total mass of the position restraint atoms is 0");
928 for (j = 0; j < npbcdim; j++)
930 com[j] = sum[j]/totmass;
932 fprintf(stderr, "The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f\n", com[XX], com[YY], com[ZZ]);
935 if (rc_scaling != erscNO)
937 assert(npbcdim <= DIM);
939 for (mb = 0; mb < mtop->nmolblock; mb++)
941 molb = &mtop->molblock[mb];
942 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
943 if (molb->nposres_xA > 0 || molb->nposres_xB > 0)
945 xp = (!bTopB ? molb->posres_xA : molb->posres_xB);
946 for (i = 0; i < nat_molb; i++)
948 for (j = 0; j < npbcdim; j++)
950 if (rc_scaling == erscALL)
952 /* Convert from Cartesian to crystal coordinates */
953 xp[i][j] *= invbox[j][j];
954 for (k = j+1; k < npbcdim; k++)
956 xp[i][j] += invbox[k][j]*xp[i][k];
959 else if (rc_scaling == erscCOM)
961 /* Subtract the center of mass */
969 if (rc_scaling == erscCOM)
971 /* Convert the COM from Cartesian to crystal coordinates */
972 for (j = 0; j < npbcdim; j++)
974 com[j] *= invbox[j][j];
975 for (k = j+1; k < npbcdim; k++)
977 com[j] += invbox[k][j]*com[k];
983 free_t_atoms(&dumat, TRUE);
989 static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
990 char *fnA, char *fnB,
991 int rc_scaling, int ePBC,
997 read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
998 /* It is safer to simply read the b-state posres rather than trying
999 * to be smart and copy the positions.
1001 read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
1004 static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
1005 t_inputrec *ir, warninp_t wi)
1008 char warn_buf[STRLEN];
1012 fprintf(stderr, "Searching the wall atom type(s)\n");
1014 for (i = 0; i < ir->nwall; i++)
1016 ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
1017 if (ir->wall_atomtype[i] == NOTSET)
1019 sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
1020 warning_error(wi, warn_buf);
1025 static int nrdf_internal(t_atoms *atoms)
1030 for (i = 0; i < atoms->nr; i++)
1032 /* Vsite ptype might not be set here yet, so also check the mass */
1033 if ((atoms->atom[i].ptype == eptAtom ||
1034 atoms->atom[i].ptype == eptNucleus)
1035 && atoms->atom[i].m > 0)
1042 case 0: nrdf = 0; break;
1043 case 1: nrdf = 0; break;
1044 case 2: nrdf = 1; break;
1045 default: nrdf = nmass*3 - 6; break;
1052 spline1d( double dx,
1064 for (i = 1; i < n-1; i++)
1066 p = 0.5*y2[i-1]+2.0;
1068 q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
1069 u[i] = (3.0*q/dx-0.5*u[i-1])/p;
1074 for (i = n-2; i >= 0; i--)
1076 y2[i] = y2[i]*y2[i+1]+u[i];
1082 interpolate1d( double xmin,
1095 a = (xmin+(ix+1)*dx-x)/dx;
1096 b = (x-xmin-ix*dx)/dx;
1098 *y = a*ya[ix]+b*ya[ix+1]+((a*a*a-a)*y2a[ix]+(b*b*b-b)*y2a[ix+1])*(dx*dx)/6.0;
1099 *y1 = (ya[ix+1]-ya[ix])/dx-(3.0*a*a-1.0)/6.0*dx*y2a[ix]+(3.0*b*b-1.0)/6.0*dx*y2a[ix+1];
1104 setup_cmap (int grid_spacing,
1107 gmx_cmap_t * cmap_grid)
1109 double *tmp_u, *tmp_u2, *tmp_yy, *tmp_y1, *tmp_t2, *tmp_grid;
1111 int i, j, k, ii, jj, kk, idx;
1113 double dx, xmin, v, v1, v2, v12;
1116 snew(tmp_u, 2*grid_spacing);
1117 snew(tmp_u2, 2*grid_spacing);
1118 snew(tmp_yy, 2*grid_spacing);
1119 snew(tmp_y1, 2*grid_spacing);
1120 snew(tmp_t2, 2*grid_spacing*2*grid_spacing);
1121 snew(tmp_grid, 2*grid_spacing*2*grid_spacing);
1123 dx = 360.0/grid_spacing;
1124 xmin = -180.0-dx*grid_spacing/2;
1126 for (kk = 0; kk < nc; kk++)
1128 /* Compute an offset depending on which cmap we are using
1129 * Offset will be the map number multiplied with the
1130 * grid_spacing * grid_spacing * 2
1132 offset = kk * grid_spacing * grid_spacing * 2;
1134 for (i = 0; i < 2*grid_spacing; i++)
1136 ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
1138 for (j = 0; j < 2*grid_spacing; j++)
1140 jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
1141 tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
1145 for (i = 0; i < 2*grid_spacing; i++)
1147 spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u, &(tmp_t2[2*grid_spacing*i]));
1150 for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
1152 ii = i-grid_spacing/2;
1155 for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
1157 jj = j-grid_spacing/2;
1160 for (k = 0; k < 2*grid_spacing; k++)
1162 interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
1163 &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
1166 spline1d(dx, tmp_yy, 2*grid_spacing, tmp_u, tmp_u2);
1167 interpolate1d(xmin, dx, tmp_yy, tmp_u2, phi, &v, &v1);
1168 spline1d(dx, tmp_y1, 2*grid_spacing, tmp_u, tmp_u2);
1169 interpolate1d(xmin, dx, tmp_y1, tmp_u2, phi, &v2, &v12);
1171 idx = ii*grid_spacing+jj;
1172 cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
1173 cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
1174 cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
1175 cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
1181 void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
1185 cmap_grid->ngrid = ngrid;
1186 cmap_grid->grid_spacing = grid_spacing;
1187 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1189 snew(cmap_grid->cmapdata, ngrid);
1191 for (i = 0; i < cmap_grid->ngrid; i++)
1193 snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
1198 static int count_constraints(gmx_mtop_t *mtop, t_molinfo *mi, warninp_t wi)
1200 int count, count_mol, i, mb;
1201 gmx_molblock_t *molb;
1206 for (mb = 0; mb < mtop->nmolblock; mb++)
1209 molb = &mtop->molblock[mb];
1210 plist = mi[molb->type].plist;
1212 for (i = 0; i < F_NRE; i++)
1216 count_mol += 3*plist[i].nr;
1218 else if (interaction_function[i].flags & IF_CONSTRAINT)
1220 count_mol += plist[i].nr;
1224 if (count_mol > nrdf_internal(&mi[molb->type].atoms))
1227 "Molecule type '%s' has %d constraints.\n"
1228 "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
1229 *mi[molb->type].name, count_mol,
1230 nrdf_internal(&mi[molb->type].atoms));
1233 count += molb->nmol*count_mol;
1239 static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
1241 int i, nmiss, natoms, mt;
1243 const t_atoms *atoms;
1246 for (mt = 0; mt < sys->nmoltype; mt++)
1248 atoms = &sys->moltype[mt].atoms;
1251 for (i = 0; i < natoms; i++)
1253 q = atoms->atom[i].q;
1254 if ((get_atomtype_radius(atoms->atom[i].type, atype) == 0 ||
1255 get_atomtype_vol(atoms->atom[i].type, atype) == 0 ||
1256 get_atomtype_surftens(atoms->atom[i].type, atype) == 0 ||
1257 get_atomtype_gb_radius(atoms->atom[i].type, atype) == 0 ||
1258 get_atomtype_S_hct(atoms->atom[i].type, atype) == 0) &&
1261 fprintf(stderr, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
1262 get_atomtype_name(atoms->atom[i].type, atype), q);
1270 gmx_fatal(FARGS, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield has parameters with value zero for %d atomtypes that occur as charged atoms.", nmiss);
1275 static void check_gbsa_params(gpp_atomtype_t atype)
1279 /* If we are doing GBSA, check that we got the parameters we need
1280 * This checking is to see if there are GBSA paratmeters for all
1281 * atoms in the force field. To go around this for testing purposes
1282 * comment out the nerror++ counter temporarily
1285 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1287 if (get_atomtype_radius(i, atype) < 0 ||
1288 get_atomtype_vol(i, atype) < 0 ||
1289 get_atomtype_surftens(i, atype) < 0 ||
1290 get_atomtype_gb_radius(i, atype) < 0 ||
1291 get_atomtype_S_hct(i, atype) < 0)
1293 fprintf(stderr, "\nGB parameter(s) missing or negative for atom type '%s'\n",
1294 get_atomtype_name(i, atype));
1301 gmx_fatal(FARGS, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for %d atomtypes or they might be negative.", nmiss);
1306 static real calc_temp(const gmx_mtop_t *mtop,
1307 const t_inputrec *ir,
1311 gmx_mtop_atomloop_all_t aloop;
1318 aloop = gmx_mtop_atomloop_all_init(mtop);
1319 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
1321 sum_mv2 += atom->m*norm2(v[a]);
1325 for (g = 0; g < ir->opts.ngtc; g++)
1327 nrdf += ir->opts.nrdf[g];
1330 return sum_mv2/(nrdf*BOLTZ);
1333 static real get_max_reference_temp(const t_inputrec *ir,
1342 for (i = 0; i < ir->opts.ngtc; i++)
1344 if (ir->opts.tau_t[i] < 0)
1350 ref_t = max(ref_t, ir->opts.ref_t[i]);
1358 sprintf(buf, "Some temperature coupling groups do not use temperature coupling. We will assume their temperature is not more than %.3f K. If their temperature is higher, the energy error and the Verlet buffer might be underestimated.",
1366 static void set_verlet_buffer(const gmx_mtop_t *mtop,
1373 verletbuf_list_setup_t ls;
1376 char warn_buf[STRLEN];
1378 printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol, buffer_temp);
1380 /* Calculate the buffer size for simple atom vs atoms list */
1381 ls.cluster_size_i = 1;
1382 ls.cluster_size_j = 1;
1383 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1384 &ls, &n_nonlin_vsite, &rlist_1x1);
1386 /* Set the pair-list buffer size in ir */
1387 verletbuf_get_list_setup(FALSE, &ls);
1388 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1389 &ls, &n_nonlin_vsite, &ir->rlist);
1391 if (n_nonlin_vsite > 0)
1393 sprintf(warn_buf, "There are %d non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly.", n_nonlin_vsite);
1394 warning_note(wi, warn_buf);
1397 printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
1398 1, 1, rlist_1x1, rlist_1x1-max(ir->rvdw, ir->rcoulomb));
1400 ir->rlistlong = ir->rlist;
1401 printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
1402 ls.cluster_size_i, ls.cluster_size_j,
1403 ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb));
1405 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
1407 gmx_fatal(FARGS, "The pair-list cut-off (%g nm) is longer than half the shortest box vector or longer than the smallest box diagonal element (%g nm). Increase the box size or decrease nstlist or increase verlet-buffer-tolerance.", ir->rlistlong, sqrt(max_cutoff2(ir->ePBC, box)));
1411 int gmx_grompp(int argc, char *argv[])
1413 static const char *desc[] = {
1414 "[THISMODULE] (the gromacs preprocessor)",
1415 "reads a molecular topology file, checks the validity of the",
1416 "file, expands the topology from a molecular description to an atomic",
1417 "description. The topology file contains information about",
1418 "molecule types and the number of molecules, the preprocessor",
1419 "copies each molecule as needed. ",
1420 "There is no limitation on the number of molecule types. ",
1421 "Bonds and bond-angles can be converted into constraints, separately",
1422 "for hydrogens and heavy atoms.",
1423 "Then a coordinate file is read and velocities can be generated",
1424 "from a Maxwellian distribution if requested.",
1425 "[THISMODULE] also reads parameters for [gmx-mdrun] ",
1426 "(eg. number of MD steps, time step, cut-off), and others such as",
1427 "NEMD parameters, which are corrected so that the net acceleration",
1429 "Eventually a binary file is produced that can serve as the sole input",
1430 "file for the MD program.[PAR]",
1432 "[THISMODULE] uses the atom names from the topology file. The atom names",
1433 "in the coordinate file (option [TT]-c[tt]) are only read to generate",
1434 "warnings when they do not match the atom names in the topology.",
1435 "Note that the atom names are irrelevant for the simulation as",
1436 "only the atom types are used for generating interaction parameters.[PAR]",
1438 "[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
1439 "etc. The preprocessor supports the following keywords:[PAR]",
1440 "#ifdef VARIABLE[BR]",
1441 "#ifndef VARIABLE[BR]",
1444 "#define VARIABLE[BR]",
1445 "#undef VARIABLE[BR]"
1446 "#include \"filename\"[BR]",
1447 "#include <filename>[PAR]",
1448 "The functioning of these statements in your topology may be modulated by",
1449 "using the following two flags in your [REF].mdp[ref] file:[PAR]",
1450 "[TT]define = -DVARIABLE1 -DVARIABLE2[tt][BR]",
1451 "[TT]include = -I/home/john/doe[tt][BR]",
1452 "For further information a C-programming textbook may help you out.",
1453 "Specifying the [TT]-pp[tt] flag will get the pre-processed",
1454 "topology file written out so that you can verify its contents.[PAR]",
1456 "When using position restraints a file with restraint coordinates",
1457 "can be supplied with [TT]-r[tt], otherwise restraining will be done",
1458 "with respect to the conformation from the [TT]-c[tt] option.",
1459 "For free energy calculation the the coordinates for the B topology",
1460 "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
1461 "those of the A topology.[PAR]",
1463 "Starting coordinates can be read from trajectory with [TT]-t[tt].",
1464 "The last frame with coordinates and velocities will be read,",
1465 "unless the [TT]-time[tt] option is used. Only if this information",
1466 "is absent will the coordinates in the [TT]-c[tt] file be used.",
1467 "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
1468 "in your [REF].mdp[ref] file. An energy file can be supplied with",
1469 "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
1472 "[THISMODULE] can be used to restart simulations (preserving",
1473 "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
1474 "However, for simply changing the number of run steps to extend",
1475 "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].",
1476 "You then supply the old checkpoint file directly to [gmx-mdrun]",
1477 "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
1478 "like output frequency, then supplying the checkpoint file to",
1479 "[THISMODULE] with [TT]-t[tt] along with a new [REF].mdp[ref] file",
1480 "with [TT]-f[tt] is the recommended procedure.[PAR]",
1482 "By default, all bonded interactions which have constant energy due to",
1483 "virtual site constructions will be removed. If this constant energy is",
1484 "not zero, this will result in a shift in the total energy. All bonded",
1485 "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
1486 "all constraints for distances which will be constant anyway because",
1487 "of virtual site constructions will be removed. If any constraints remain",
1488 "which involve virtual sites, a fatal error will result.[PAR]"
1490 "To verify your run input file, please take note of all warnings",
1491 "on the screen, and correct where necessary. Do also look at the contents",
1492 "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
1493 "the input that [THISMODULE] has read. If in doubt, you can start [THISMODULE]",
1494 "with the [TT]-debug[tt] option which will give you more information",
1495 "in a file called [TT]grompp.log[tt] (along with real debug info). You",
1496 "can see the contents of the run input file with the [gmx-dump]",
1497 "program. [gmx-check] can be used to compare the contents of two",
1498 "run input files.[PAR]"
1500 "The [TT]-maxwarn[tt] option can be used to override warnings printed",
1501 "by [THISMODULE] that otherwise halt output. In some cases, warnings are",
1502 "harmless, but usually they are not. The user is advised to carefully",
1503 "interpret the output messages before attempting to bypass them with",
1510 gpp_atomtype_t atype;
1512 int natoms, nvsite, comb, mt;
1516 real max_spacing, fudgeQQ;
1518 char fn[STRLEN], fnB[STRLEN];
1519 const char *mdparin;
1521 gmx_bool bNeedVel, bGenVel;
1522 gmx_bool have_atomnumber;
1524 t_params *gb_plist = NULL;
1525 gmx_genborn_t *born = NULL;
1527 gmx_bool bVerbose = FALSE;
1529 char warn_buf[STRLEN];
1531 t_atoms IMDatoms; /* Atoms to be operated on interactively (IMD) */
1534 { efMDP, NULL, NULL, ffREAD },
1535 { efMDP, "-po", "mdout", ffWRITE },
1536 { efSTX, "-c", NULL, ffREAD },
1537 { efSTX, "-r", NULL, ffOPTRD },
1538 { efSTX, "-rb", NULL, ffOPTRD },
1539 { efNDX, NULL, NULL, ffOPTRD },
1540 { efTOP, NULL, NULL, ffREAD },
1541 { efTOP, "-pp", "processed", ffOPTWR },
1542 { efTPR, "-o", NULL, ffWRITE },
1543 { efTRN, "-t", NULL, ffOPTRD },
1544 { efEDR, "-e", NULL, ffOPTRD },
1545 /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
1546 { efGRO, "-imd", "imdgroup", ffOPTWR },
1547 { efTRN, "-ref", "rotref", ffOPTRW }
1549 #define NFILE asize(fnm)
1551 /* Command line options */
1552 static gmx_bool bRenum = TRUE;
1553 static gmx_bool bRmVSBds = TRUE, bZero = FALSE;
1554 static int i, maxwarn = 0;
1555 static real fr_time = -1;
1557 { "-v", FALSE, etBOOL, {&bVerbose},
1558 "Be loud and noisy" },
1559 { "-time", FALSE, etREAL, {&fr_time},
1560 "Take frame at or first after this time." },
1561 { "-rmvsbds", FALSE, etBOOL, {&bRmVSBds},
1562 "Remove constant bonded interactions with virtual sites" },
1563 { "-maxwarn", FALSE, etINT, {&maxwarn},
1564 "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
1565 { "-zero", FALSE, etBOOL, {&bZero},
1566 "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
1567 { "-renum", FALSE, etBOOL, {&bRenum},
1568 "Renumber atomtypes and minimize number of atomtypes" }
1571 /* Initiate some variables */
1576 /* Parse the command line */
1577 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
1578 asize(desc), desc, 0, NULL, &oenv))
1583 wi = init_warning(TRUE, maxwarn);
1585 /* PARAMETER file processing */
1586 mdparin = opt2fn("-f", NFILE, fnm);
1587 set_warning_line(wi, mdparin, -1);
1588 get_ir(mdparin, opt2fn("-po", NFILE, fnm), ir, opts, wi);
1592 fprintf(stderr, "checking input for internal consistency...\n");
1594 check_ir(mdparin, ir, opts, wi);
1596 if (ir->ld_seed == -1)
1598 ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed();
1599 fprintf(stderr, "Setting the LD random seed to %"GMX_PRId64 "\n", ir->ld_seed);
1602 if (ir->expandedvals->lmc_seed == -1)
1604 ir->expandedvals->lmc_seed = (int)gmx_rng_make_seed();
1605 fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
1608 bNeedVel = EI_STATE_VELOCITY(ir->eI);
1609 bGenVel = (bNeedVel && opts->bGenVel);
1610 if (bGenVel && ir->bContinuation)
1613 "Generating velocities is inconsistent with attempting "
1614 "to continue a previous run. Choose only one of "
1615 "gen-vel = yes and continuation = yes.");
1616 warning_error(wi, warn_buf);
1622 atype = init_atomtype();
1625 pr_symtab(debug, 0, "Just opened", &sys->symtab);
1628 strcpy(fn, ftp2fn(efTOP, NFILE, fnm));
1629 if (!gmx_fexist(fn))
1631 gmx_fatal(FARGS, "%s does not exist", fn);
1633 new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
1634 opts, ir, bZero, bGenVel, bVerbose, &state,
1635 atype, sys, &nmi, &mi, plist, &comb, &reppow, &fudgeQQ,
1641 pr_symtab(debug, 0, "After new_status", &sys->symtab);
1645 /* set parameters for virtual site construction (not for vsiten) */
1646 for (mt = 0; mt < sys->nmoltype; mt++)
1649 set_vsites(bVerbose, &sys->moltype[mt].atoms, atype, mi[mt].plist);
1651 /* now throw away all obsolete bonds, angles and dihedrals: */
1652 /* note: constraints are ALWAYS removed */
1655 for (mt = 0; mt < sys->nmoltype; mt++)
1657 clean_vsite_bondeds(mi[mt].plist, sys->moltype[mt].atoms.nr, bRmVSBds);
1661 if (nvsite && ir->eI == eiNM)
1663 gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
1666 if (ir->cutoff_scheme == ecutsVERLET)
1668 fprintf(stderr, "Removing all charge groups because cutoff-scheme=%s\n",
1669 ecutscheme_names[ir->cutoff_scheme]);
1671 /* Remove all charge groups */
1672 gmx_mtop_remove_chargegroups(sys);
1675 if (count_constraints(sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
1677 if (ir->eI == eiCG || ir->eI == eiLBFGS)
1679 sprintf(warn_buf, "Can not do %s with %s, use %s",
1680 EI(ir->eI), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1681 warning_error(wi, warn_buf);
1683 if (ir->bPeriodicMols)
1685 sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
1686 econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1687 warning_error(wi, warn_buf);
1691 if (EI_SD (ir->eI) && ir->etc != etcNO)
1693 warning_note(wi, "Temperature coupling is ignored with SD integrators.");
1696 /* If we are doing QM/MM, check that we got the atom numbers */
1697 have_atomnumber = TRUE;
1698 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1700 have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
1702 if (!have_atomnumber && ir->bQMMM)
1706 "It appears as if you are trying to run a QM/MM calculation, but the force\n"
1707 "field you are using does not contain atom numbers fields. This is an\n"
1708 "optional field (introduced in Gromacs 3.3) for general runs, but mandatory\n"
1709 "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
1710 "an integer just before the mass column in ffXXXnb.itp.\n"
1711 "NB: United atoms have the same atom numbers as normal ones.\n\n");
1716 if ((ir->adress->const_wf > 1) || (ir->adress->const_wf < 0))
1718 warning_error(wi, "AdResS contant weighting function should be between 0 and 1\n\n");
1720 /** TODO check size of ex+hy width against box size */
1723 /* Check for errors in the input now, since they might cause problems
1724 * during processing further down.
1726 check_warning_error(wi, FARGS);
1728 if (opt2bSet("-r", NFILE, fnm))
1730 sprintf(fn, "%s", opt2fn("-r", NFILE, fnm));
1734 sprintf(fn, "%s", opt2fn("-c", NFILE, fnm));
1736 if (opt2bSet("-rb", NFILE, fnm))
1738 sprintf(fnB, "%s", opt2fn("-rb", NFILE, fnm));
1745 if (nint_ftype(sys, mi, F_POSRES) > 0 || nint_ftype(sys, mi, F_FBPOSRES) > 0)
1749 fprintf(stderr, "Reading position restraint coords from %s", fn);
1750 if (strcmp(fn, fnB) == 0)
1752 fprintf(stderr, "\n");
1756 fprintf(stderr, " and %s\n", fnB);
1759 gen_posres(sys, mi, fn, fnB,
1760 ir->refcoord_scaling, ir->ePBC,
1761 ir->posres_com, ir->posres_comB,
1765 /* If we are using CMAP, setup the pre-interpolation grid */
1766 if (plist[F_CMAP].ncmap > 0)
1768 init_cmap_grid(&sys->ffparams.cmap_grid, plist[F_CMAP].nc, plist[F_CMAP].grid_spacing);
1769 setup_cmap(plist[F_CMAP].grid_spacing, plist[F_CMAP].nc, plist[F_CMAP].cmap, &sys->ffparams.cmap_grid);
1772 set_wall_atomtype(atype, opts, ir, wi);
1775 renum_atype(plist, sys, ir->wall_atomtype, atype, bVerbose);
1776 ntype = get_atomtype_ntypes(atype);
1779 if (ir->implicit_solvent != eisNO)
1781 /* Now we have renumbered the atom types, we can check the GBSA params */
1782 check_gbsa_params(atype);
1784 /* Check that all atoms that have charge and/or LJ-parameters also have
1785 * sensible GB-parameters
1787 check_gbsa_params_charged(sys, atype);
1790 /* PELA: Copy the atomtype data to the topology atomtype list */
1791 copy_atomtype_atomtypes(atype, &(sys->atomtypes));
1795 pr_symtab(debug, 0, "After renum_atype", &sys->symtab);
1800 fprintf(stderr, "converting bonded parameters...\n");
1803 ntype = get_atomtype_ntypes(atype);
1804 convert_params(ntype, plist, mi, comb, reppow, fudgeQQ, sys);
1808 pr_symtab(debug, 0, "After convert_params", &sys->symtab);
1811 /* set ptype to VSite for virtual sites */
1812 for (mt = 0; mt < sys->nmoltype; mt++)
1814 set_vsites_ptype(FALSE, &sys->moltype[mt]);
1818 pr_symtab(debug, 0, "After virtual sites", &sys->symtab);
1820 /* Check velocity for virtual sites and shells */
1823 check_vel(sys, state.v);
1826 /* check for shells and inpurecs */
1827 check_shells_inputrec(sys, ir, wi);
1832 for (i = 0; i < sys->nmoltype; i++)
1834 check_cg_sizes(ftp2fn(efTOP, NFILE, fnm), &sys->moltype[i].cgs, wi);
1837 if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
1839 check_bonds_timestep(sys, ir->delta_t, wi);
1842 if (EI_ENERGY_MINIMIZATION(ir->eI) && 0 == ir->nsteps)
1844 warning_note(wi, "Zero-step energy minimization will alter the coordinates before calculating the energy. If you just want the energy of a single point, try zero-step MD (with unconstrained_start = yes). To do multiple single-point energy evaluations of different configurations of the same topology, use mdrun -rerun.");
1847 check_warning_error(wi, FARGS);
1851 fprintf(stderr, "initialising group options...\n");
1853 do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
1855 bGenVel ? state.v : NULL,
1858 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 &&
1861 if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
1865 if (EI_MD(ir->eI) && ir->etc == etcNO)
1869 buffer_temp = opts->tempi;
1873 buffer_temp = calc_temp(sys, ir, state.v);
1875 if (buffer_temp > 0)
1877 sprintf(warn_buf, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp);
1878 warning_note(wi, warn_buf);
1882 sprintf(warn_buf, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
1883 (int)(verlet_buffer_ratio_NVE_T0*100 + 0.5));
1884 warning_note(wi, warn_buf);
1889 buffer_temp = get_max_reference_temp(ir, wi);
1892 if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
1894 /* NVE with initial T=0: we add a fixed ratio to rlist.
1895 * Since we don't actually use verletbuf_tol, we set it to -1
1896 * so it can't be misused later.
1898 ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
1899 ir->verletbuf_tol = -1;
1903 /* We warn for NVE simulations with >1(.1)% drift tolerance */
1904 const real drift_tol = 0.01;
1907 /* We use 2 DOF per atom = 2kT pot+kin energy, to be on
1908 * the safe side with constraints (without constraints: 3 DOF).
1910 ener_runtime = 2*BOLTZ*buffer_temp/(ir->nsteps*ir->delta_t);
1912 if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 &&
1914 ir->verletbuf_tol > 1.1*drift_tol*ener_runtime)
1916 sprintf(warn_buf, "You are using a Verlet buffer tolerance of %g kJ/mol/ps for an NVE simulation of length %g ps, which can give a final drift of %d%%. For conserving energy to %d%%, you might need to set verlet-buffer-tolerance to %.1e.",
1917 ir->verletbuf_tol, ir->nsteps*ir->delta_t,
1918 (int)(ir->verletbuf_tol/ener_runtime*100 + 0.5),
1919 (int)(100*drift_tol + 0.5),
1920 drift_tol*ener_runtime);
1921 warning_note(wi, warn_buf);
1924 set_verlet_buffer(sys, ir, buffer_temp, state.box, wi);
1929 /* Init the temperature coupling state */
1930 init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
1934 fprintf(stderr, "Checking consistency between energy and charge groups...\n");
1936 check_eg_vs_cg(sys);
1940 pr_symtab(debug, 0, "After index", &sys->symtab);
1943 triple_check(mdparin, ir, sys, wi);
1944 close_symtab(&sys->symtab);
1947 pr_symtab(debug, 0, "After close", &sys->symtab);
1950 /* make exclusions between QM atoms */
1953 if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
1955 gmx_fatal(FARGS, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
1959 generate_qmexcl(sys, ir, wi);
1963 if (ftp2bSet(efTRN, NFILE, fnm))
1967 fprintf(stderr, "getting data from old trajectory ...\n");
1969 cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
1970 bNeedVel, bGenVel, fr_time, ir, &state, sys, oenv);
1973 if (ir->ePBC == epbcXY && ir->nwall != 2)
1975 clear_rvec(state.box[ZZ]);
1978 if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
1980 set_warning_line(wi, mdparin, -1);
1981 check_chargegroup_radii(sys, ir, state.x, wi);
1984 if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1986 /* Calculate the optimal grid dimensions */
1987 copy_mat(state.box, box);
1988 if (ir->ePBC == epbcXY && ir->nwall == 2)
1990 svmul(ir->wall_ewald_zfac, box[ZZ], box[ZZ]);
1992 if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
1994 /* Mark fourier_spacing as not used */
1995 ir->fourier_spacing = 0;
1997 else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
1999 set_warning_line(wi, mdparin, -1);
2000 warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
2002 max_spacing = calc_grid(stdout, box, ir->fourier_spacing,
2003 &(ir->nkx), &(ir->nky), &(ir->nkz));
2006 /* MRS: eventually figure out better logic for initializing the fep
2007 values that makes declaring the lambda and declaring the state not
2008 potentially conflict if not handled correctly. */
2009 if (ir->efep != efepNO)
2011 state.fep_state = ir->fepvals->init_fep_state;
2012 for (i = 0; i < efptNR; i++)
2014 /* init_lambda trumps state definitions*/
2015 if (ir->fepvals->init_lambda >= 0)
2017 state.lambda[i] = ir->fepvals->init_lambda;
2021 if (ir->fepvals->all_lambda[i] == NULL)
2023 gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
2027 state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
2033 if (ir->ePull != epullNO)
2035 set_pull_init(ir, sys, state.x, state.box, state.lambda[efptMASS], oenv, opts->pull_start);
2040 set_reference_positions(ir->rot, state.x, state.box,
2041 opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
2045 /* reset_multinr(sys); */
2047 if (EEL_PME(ir->coulombtype))
2049 float ratio = pme_load_estimate(sys, ir, state.box);
2050 fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
2051 /* With free energy we might need to do PME both for the A and B state
2052 * charges. This will double the cost, but the optimal performance will
2053 * then probably be at a slightly larger cut-off and grid spacing.
2055 if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
2056 (ir->efep != efepNO && ratio > 2.0/3.0))
2059 "The optimal PME mesh load for parallel simulations is below 0.5\n"
2060 "and for highly parallel simulations between 0.25 and 0.33,\n"
2061 "for higher performance, increase the cut-off and the PME grid spacing.\n");
2062 if (ir->efep != efepNO)
2065 "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
2071 char warn_buf[STRLEN];
2072 double cio = compute_io(ir, sys->natoms, &sys->groups, F_NRE, 1);
2073 sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
2076 set_warning_line(wi, mdparin, -1);
2077 warning_note(wi, warn_buf);
2081 printf("%s\n", warn_buf);
2087 fprintf(stderr, "writing run input file...\n");
2090 done_warning(wi, FARGS);
2091 write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);
2093 /* Output IMD group, if bIMD is TRUE */
2094 write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
2096 done_atomtype(atype);
2097 done_mtop(sys, TRUE);
2098 done_inputrec_strings();