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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/convparm.h"
58 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
59 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
60 #include "gromacs/gmxpreprocess/grompp-impl.h"
61 #include "gromacs/gmxpreprocess/readir.h"
62 #include "gromacs/gmxpreprocess/sortwater.h"
63 #include "gromacs/gmxpreprocess/tomorse.h"
64 #include "gromacs/gmxpreprocess/topio.h"
65 #include "gromacs/gmxpreprocess/toputil.h"
66 #include "gromacs/gmxpreprocess/vsite_parm.h"
67 #include "gromacs/imd/imd.h"
68 #include "gromacs/legacyheaders/calcgrid.h"
69 #include "gromacs/legacyheaders/genborn.h"
70 #include "gromacs/legacyheaders/macros.h"
71 #include "gromacs/legacyheaders/names.h"
72 #include "gromacs/legacyheaders/perf_est.h"
73 #include "gromacs/legacyheaders/splitter.h"
74 #include "gromacs/legacyheaders/txtdump.h"
75 #include "gromacs/legacyheaders/warninp.h"
76 #include "gromacs/math/vec.h"
77 #include "gromacs/mdlib/calc_verletbuf.h"
78 #include "gromacs/mdlib/compute_io.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_molinfo **intermolecular_interactions,
504 int *comb, double *reppow, real *fudgeQQ,
508 t_molinfo *molinfo = NULL;
510 gmx_molblock_t *molblock, *molbs;
512 int mb, i, nrmols, nmismatch;
514 gmx_bool bGB = FALSE;
515 char warn_buf[STRLEN];
519 /* Set gmx_boolean for GB */
520 if (ir->implicit_solvent)
525 /* TOPOLOGY processing */
526 sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
527 plist, comb, reppow, fudgeQQ,
528 atype, &nrmols, &molinfo, intermolecular_interactions,
530 &nmolblock, &molblock, bGB,
534 snew(sys->molblock, nmolblock);
537 for (mb = 0; mb < nmolblock; mb++)
539 if (sys->nmolblock > 0 &&
540 molblock[mb].type == sys->molblock[sys->nmolblock-1].type)
542 /* Merge consecutive blocks with the same molecule type */
543 sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
544 sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
546 else if (molblock[mb].nmol > 0)
548 /* Add a new molblock to the topology */
549 molbs = &sys->molblock[sys->nmolblock];
550 *molbs = molblock[mb];
551 molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
552 molbs->nposres_xA = 0;
553 molbs->nposres_xB = 0;
554 sys->natoms += molbs->nmol*molbs->natoms_mol;
558 if (sys->nmolblock == 0)
560 gmx_fatal(FARGS, "No molecules were defined in the system");
563 renumber_moltypes(sys, &nrmols, &molinfo);
567 convert_harmonics(nrmols, molinfo, atype);
570 if (ir->eDisre == edrNone)
572 i = rm_interactions(F_DISRES, nrmols, molinfo);
575 set_warning_line(wi, "unknown", -1);
576 sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
577 warning_note(wi, warn_buf);
580 if (opts->bOrire == FALSE)
582 i = rm_interactions(F_ORIRES, nrmols, molinfo);
585 set_warning_line(wi, "unknown", -1);
586 sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
587 warning_note(wi, warn_buf);
591 /* Copy structures from msys to sys */
592 molinfo2mtop(nrmols, molinfo, sys);
594 gmx_mtop_finalize(sys);
596 /* COORDINATE file processing */
599 fprintf(stderr, "processing coordinates...\n");
602 get_stx_coordnum(confin, &state->natoms);
603 if (state->natoms != sys->natoms)
605 gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
606 " does not match topology (%s, %d)",
607 confin, state->natoms, topfile, sys->natoms);
611 /* make space for coordinates and velocities */
614 init_t_atoms(confat, state->natoms, FALSE);
615 init_state(state, state->natoms, 0, 0, 0, 0);
616 read_stx_conf(confin, title, confat, state->x, state->v, NULL, state->box);
617 /* This call fixes the box shape for runs with pressure scaling */
618 set_box_rel(ir, state);
620 nmismatch = check_atom_names(topfile, confin, sys, confat);
621 free_t_atoms(confat, TRUE);
626 sprintf(buf, "%d non-matching atom name%s\n"
627 "atom names from %s will be used\n"
628 "atom names from %s will be ignored\n",
629 nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
633 /* Do more checks, mostly related to constraints */
636 fprintf(stderr, "double-checking input for internal consistency...\n");
639 int bHasNormalConstraints = 0 < (nint_ftype(sys, molinfo, F_CONSTR) +
640 nint_ftype(sys, molinfo, F_CONSTRNC));
641 int bHasAnyConstraints = bHasNormalConstraints || 0 < nint_ftype(sys, molinfo, F_SETTLE);
642 double_check(ir, state->box,
643 bHasNormalConstraints,
652 gmx_mtop_atomloop_all_t aloop;
656 snew(mass, state->natoms);
657 aloop = gmx_mtop_atomloop_all_init(sys);
658 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
664 if (opts->seed == -1)
666 useed = (int)gmx_rng_make_seed();
667 fprintf(stderr, "Setting gen_seed to %u\n", useed);
669 maxwell_speed(opts->tempi, useed, sys, state->v);
671 stop_cm(stdout, state->natoms, mass, state->x, state->v);
679 static void copy_state(const char *slog, t_trxframe *fr,
680 gmx_bool bReadVel, t_state *state,
685 if (fr->not_ok & FRAME_NOT_OK)
687 gmx_fatal(FARGS, "Can not start from an incomplete frame");
691 gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s",
695 for (i = 0; i < state->natoms; i++)
697 copy_rvec(fr->x[i], state->x[i]);
703 gmx_incons("Trajecory frame unexpectedly does not contain velocities");
705 for (i = 0; i < state->natoms; i++)
707 copy_rvec(fr->v[i], state->v[i]);
712 copy_mat(fr->box, state->box);
715 *use_time = fr->time;
718 static void cont_status(const char *slog, const char *ener,
719 gmx_bool bNeedVel, gmx_bool bGenVel, real fr_time,
720 t_inputrec *ir, t_state *state,
722 const output_env_t oenv)
723 /* If fr_time == -1 read the last frame available which is complete */
731 bReadVel = (bNeedVel && !bGenVel);
734 "Reading Coordinates%s and Box size from old trajectory\n",
735 bReadVel ? ", Velocities" : "");
738 fprintf(stderr, "Will read whole trajectory\n");
742 fprintf(stderr, "Will read till time %g\n", fr_time);
748 fprintf(stderr, "Velocities generated: "
749 "ignoring velocities in input trajectory\n");
751 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
755 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X | TRX_NEED_V);
761 "WARNING: Did not find a frame with velocities in file %s,\n"
762 " all velocities will be set to zero!\n\n", slog);
763 for (i = 0; i < sys->natoms; i++)
765 clear_rvec(state->v[i]);
768 /* Search for a frame without velocities */
770 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
774 state->natoms = fr.natoms;
776 if (sys->natoms != state->natoms)
778 gmx_fatal(FARGS, "Number of atoms in Topology "
779 "is not the same as in Trajectory");
781 copy_state(slog, &fr, bReadVel, state, &use_time);
783 /* Find the appropriate frame */
784 while ((fr_time == -1 || fr.time < fr_time) &&
785 read_next_frame(oenv, fp, &fr))
787 copy_state(slog, &fr, bReadVel, state, &use_time);
792 /* Set the relative box lengths for preserving the box shape.
793 * Note that this call can lead to differences in the last bit
794 * with respect to using gmx convert-tpr to create a [REF].tpx[ref] file.
796 set_box_rel(ir, state);
798 fprintf(stderr, "Using frame at t = %g ps\n", use_time);
799 fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
801 if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
803 get_enx_state(ener, use_time, &sys->groups, ir, state);
804 preserve_box_shape(ir, state->box_rel, state->boxv);
808 static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
810 int rc_scaling, int ePBC,
814 gmx_bool bFirst = TRUE, *hadAtom;
820 int natoms, npbcdim = 0;
821 char warn_buf[STRLEN], title[STRLEN];
822 int a, i, ai, j, k, mb, nat_molb;
823 gmx_molblock_t *molb;
827 get_stx_coordnum(fn, &natoms);
828 if (natoms != mtop->natoms)
830 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);
831 warning(wi, warn_buf);
835 init_t_atoms(&dumat, natoms, FALSE);
836 read_stx_conf(fn, title, &dumat, x, v, NULL, box);
838 npbcdim = ePBC2npbcdim(ePBC);
840 if (rc_scaling != erscNO)
842 copy_mat(box, invbox);
843 for (j = npbcdim; j < DIM; j++)
845 clear_rvec(invbox[j]);
848 m_inv_ur0(invbox, invbox);
851 /* Copy the reference coordinates to mtop */
855 snew(hadAtom, natoms);
856 for (mb = 0; mb < mtop->nmolblock; mb++)
858 molb = &mtop->molblock[mb];
859 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
860 pr = &(molinfo[molb->type].plist[F_POSRES]);
861 prfb = &(molinfo[molb->type].plist[F_FBPOSRES]);
862 if (pr->nr > 0 || prfb->nr > 0)
864 atom = mtop->moltype[molb->type].atoms.atom;
865 for (i = 0; (i < pr->nr); i++)
867 ai = pr->param[i].AI;
870 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
871 ai+1, *molinfo[molb->type].name, fn, natoms);
874 if (rc_scaling == erscCOM)
876 /* Determine the center of mass of the posres reference coordinates */
877 for (j = 0; j < npbcdim; j++)
879 sum[j] += atom[ai].m*x[a+ai][j];
881 totmass += atom[ai].m;
884 /* Same for flat-bottomed posres, but do not count an atom twice for COM */
885 for (i = 0; (i < prfb->nr); i++)
887 ai = prfb->param[i].AI;
890 gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
891 ai+1, *molinfo[molb->type].name, fn, natoms);
893 if (rc_scaling == erscCOM && hadAtom[ai] == FALSE)
895 /* Determine the center of mass of the posres reference coordinates */
896 for (j = 0; j < npbcdim; j++)
898 sum[j] += atom[ai].m*x[a+ai][j];
900 totmass += atom[ai].m;
905 molb->nposres_xA = nat_molb;
906 snew(molb->posres_xA, molb->nposres_xA);
907 for (i = 0; i < nat_molb; i++)
909 copy_rvec(x[a+i], molb->posres_xA[i]);
914 molb->nposres_xB = nat_molb;
915 snew(molb->posres_xB, molb->nposres_xB);
916 for (i = 0; i < nat_molb; i++)
918 copy_rvec(x[a+i], molb->posres_xB[i]);
924 if (rc_scaling == erscCOM)
928 gmx_fatal(FARGS, "The total mass of the position restraint atoms is 0");
930 for (j = 0; j < npbcdim; j++)
932 com[j] = sum[j]/totmass;
934 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]);
937 if (rc_scaling != erscNO)
939 assert(npbcdim <= DIM);
941 for (mb = 0; mb < mtop->nmolblock; mb++)
943 molb = &mtop->molblock[mb];
944 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
945 if (molb->nposres_xA > 0 || molb->nposres_xB > 0)
947 xp = (!bTopB ? molb->posres_xA : molb->posres_xB);
948 for (i = 0; i < nat_molb; i++)
950 for (j = 0; j < npbcdim; j++)
952 if (rc_scaling == erscALL)
954 /* Convert from Cartesian to crystal coordinates */
955 xp[i][j] *= invbox[j][j];
956 for (k = j+1; k < npbcdim; k++)
958 xp[i][j] += invbox[k][j]*xp[i][k];
961 else if (rc_scaling == erscCOM)
963 /* Subtract the center of mass */
971 if (rc_scaling == erscCOM)
973 /* Convert the COM from Cartesian to crystal coordinates */
974 for (j = 0; j < npbcdim; j++)
976 com[j] *= invbox[j][j];
977 for (k = j+1; k < npbcdim; k++)
979 com[j] += invbox[k][j]*com[k];
985 free_t_atoms(&dumat, TRUE);
991 static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
992 char *fnA, char *fnB,
993 int rc_scaling, int ePBC,
999 read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
1000 /* It is safer to simply read the b-state posres rather than trying
1001 * to be smart and copy the positions.
1003 read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
1006 static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
1007 t_inputrec *ir, warninp_t wi)
1010 char warn_buf[STRLEN];
1014 fprintf(stderr, "Searching the wall atom type(s)\n");
1016 for (i = 0; i < ir->nwall; i++)
1018 ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
1019 if (ir->wall_atomtype[i] == NOTSET)
1021 sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
1022 warning_error(wi, warn_buf);
1027 static int nrdf_internal(t_atoms *atoms)
1032 for (i = 0; i < atoms->nr; i++)
1034 /* Vsite ptype might not be set here yet, so also check the mass */
1035 if ((atoms->atom[i].ptype == eptAtom ||
1036 atoms->atom[i].ptype == eptNucleus)
1037 && atoms->atom[i].m > 0)
1044 case 0: nrdf = 0; break;
1045 case 1: nrdf = 0; break;
1046 case 2: nrdf = 1; break;
1047 default: nrdf = nmass*3 - 6; break;
1054 spline1d( double dx,
1066 for (i = 1; i < n-1; i++)
1068 p = 0.5*y2[i-1]+2.0;
1070 q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
1071 u[i] = (3.0*q/dx-0.5*u[i-1])/p;
1076 for (i = n-2; i >= 0; i--)
1078 y2[i] = y2[i]*y2[i+1]+u[i];
1084 interpolate1d( double xmin,
1097 a = (xmin+(ix+1)*dx-x)/dx;
1098 b = (x-xmin-ix*dx)/dx;
1100 *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;
1101 *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];
1106 setup_cmap (int grid_spacing,
1109 gmx_cmap_t * cmap_grid)
1111 double *tmp_u, *tmp_u2, *tmp_yy, *tmp_y1, *tmp_t2, *tmp_grid;
1113 int i, j, k, ii, jj, kk, idx;
1115 double dx, xmin, v, v1, v2, v12;
1118 snew(tmp_u, 2*grid_spacing);
1119 snew(tmp_u2, 2*grid_spacing);
1120 snew(tmp_yy, 2*grid_spacing);
1121 snew(tmp_y1, 2*grid_spacing);
1122 snew(tmp_t2, 2*grid_spacing*2*grid_spacing);
1123 snew(tmp_grid, 2*grid_spacing*2*grid_spacing);
1125 dx = 360.0/grid_spacing;
1126 xmin = -180.0-dx*grid_spacing/2;
1128 for (kk = 0; kk < nc; kk++)
1130 /* Compute an offset depending on which cmap we are using
1131 * Offset will be the map number multiplied with the
1132 * grid_spacing * grid_spacing * 2
1134 offset = kk * grid_spacing * grid_spacing * 2;
1136 for (i = 0; i < 2*grid_spacing; i++)
1138 ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
1140 for (j = 0; j < 2*grid_spacing; j++)
1142 jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
1143 tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
1147 for (i = 0; i < 2*grid_spacing; i++)
1149 spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u, &(tmp_t2[2*grid_spacing*i]));
1152 for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
1154 ii = i-grid_spacing/2;
1157 for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
1159 jj = j-grid_spacing/2;
1162 for (k = 0; k < 2*grid_spacing; k++)
1164 interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
1165 &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
1168 spline1d(dx, tmp_yy, 2*grid_spacing, tmp_u, tmp_u2);
1169 interpolate1d(xmin, dx, tmp_yy, tmp_u2, phi, &v, &v1);
1170 spline1d(dx, tmp_y1, 2*grid_spacing, tmp_u, tmp_u2);
1171 interpolate1d(xmin, dx, tmp_y1, tmp_u2, phi, &v2, &v12);
1173 idx = ii*grid_spacing+jj;
1174 cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
1175 cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
1176 cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
1177 cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
1183 void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
1187 cmap_grid->ngrid = ngrid;
1188 cmap_grid->grid_spacing = grid_spacing;
1189 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1191 snew(cmap_grid->cmapdata, ngrid);
1193 for (i = 0; i < cmap_grid->ngrid; i++)
1195 snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
1200 static int count_constraints(gmx_mtop_t *mtop, t_molinfo *mi, warninp_t wi)
1202 int count, count_mol, i, mb;
1203 gmx_molblock_t *molb;
1208 for (mb = 0; mb < mtop->nmolblock; mb++)
1211 molb = &mtop->molblock[mb];
1212 plist = mi[molb->type].plist;
1214 for (i = 0; i < F_NRE; i++)
1218 count_mol += 3*plist[i].nr;
1220 else if (interaction_function[i].flags & IF_CONSTRAINT)
1222 count_mol += plist[i].nr;
1226 if (count_mol > nrdf_internal(&mi[molb->type].atoms))
1229 "Molecule type '%s' has %d constraints.\n"
1230 "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
1231 *mi[molb->type].name, count_mol,
1232 nrdf_internal(&mi[molb->type].atoms));
1235 count += molb->nmol*count_mol;
1241 static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
1243 int i, nmiss, natoms, mt;
1245 const t_atoms *atoms;
1248 for (mt = 0; mt < sys->nmoltype; mt++)
1250 atoms = &sys->moltype[mt].atoms;
1253 for (i = 0; i < natoms; i++)
1255 q = atoms->atom[i].q;
1256 if ((get_atomtype_radius(atoms->atom[i].type, atype) == 0 ||
1257 get_atomtype_vol(atoms->atom[i].type, atype) == 0 ||
1258 get_atomtype_surftens(atoms->atom[i].type, atype) == 0 ||
1259 get_atomtype_gb_radius(atoms->atom[i].type, atype) == 0 ||
1260 get_atomtype_S_hct(atoms->atom[i].type, atype) == 0) &&
1263 fprintf(stderr, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
1264 get_atomtype_name(atoms->atom[i].type, atype), q);
1272 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);
1277 static void check_gbsa_params(gpp_atomtype_t atype)
1281 /* If we are doing GBSA, check that we got the parameters we need
1282 * This checking is to see if there are GBSA paratmeters for all
1283 * atoms in the force field. To go around this for testing purposes
1284 * comment out the nerror++ counter temporarily
1287 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1289 if (get_atomtype_radius(i, atype) < 0 ||
1290 get_atomtype_vol(i, atype) < 0 ||
1291 get_atomtype_surftens(i, atype) < 0 ||
1292 get_atomtype_gb_radius(i, atype) < 0 ||
1293 get_atomtype_S_hct(i, atype) < 0)
1295 fprintf(stderr, "\nGB parameter(s) missing or negative for atom type '%s'\n",
1296 get_atomtype_name(i, atype));
1303 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);
1308 static real calc_temp(const gmx_mtop_t *mtop,
1309 const t_inputrec *ir,
1313 gmx_mtop_atomloop_all_t aloop;
1320 aloop = gmx_mtop_atomloop_all_init(mtop);
1321 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
1323 sum_mv2 += atom->m*norm2(v[a]);
1327 for (g = 0; g < ir->opts.ngtc; g++)
1329 nrdf += ir->opts.nrdf[g];
1332 return sum_mv2/(nrdf*BOLTZ);
1335 static real get_max_reference_temp(const t_inputrec *ir,
1344 for (i = 0; i < ir->opts.ngtc; i++)
1346 if (ir->opts.tau_t[i] < 0)
1352 ref_t = max(ref_t, ir->opts.ref_t[i]);
1360 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.",
1368 static void set_verlet_buffer(const gmx_mtop_t *mtop,
1375 verletbuf_list_setup_t ls;
1378 char warn_buf[STRLEN];
1380 printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol, buffer_temp);
1382 /* Calculate the buffer size for simple atom vs atoms list */
1383 ls.cluster_size_i = 1;
1384 ls.cluster_size_j = 1;
1385 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1386 &ls, &n_nonlin_vsite, &rlist_1x1);
1388 /* Set the pair-list buffer size in ir */
1389 verletbuf_get_list_setup(FALSE, &ls);
1390 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1391 &ls, &n_nonlin_vsite, &ir->rlist);
1393 if (n_nonlin_vsite > 0)
1395 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);
1396 warning_note(wi, warn_buf);
1399 printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
1400 1, 1, rlist_1x1, rlist_1x1-max(ir->rvdw, ir->rcoulomb));
1402 ir->rlistlong = ir->rlist;
1403 printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
1404 ls.cluster_size_i, ls.cluster_size_j,
1405 ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb));
1407 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
1409 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)));
1413 int gmx_grompp(int argc, char *argv[])
1415 static const char *desc[] = {
1416 "[THISMODULE] (the gromacs preprocessor)",
1417 "reads a molecular topology file, checks the validity of the",
1418 "file, expands the topology from a molecular description to an atomic",
1419 "description. The topology file contains information about",
1420 "molecule types and the number of molecules, the preprocessor",
1421 "copies each molecule as needed. ",
1422 "There is no limitation on the number of molecule types. ",
1423 "Bonds and bond-angles can be converted into constraints, separately",
1424 "for hydrogens and heavy atoms.",
1425 "Then a coordinate file is read and velocities can be generated",
1426 "from a Maxwellian distribution if requested.",
1427 "[THISMODULE] also reads parameters for [gmx-mdrun] ",
1428 "(eg. number of MD steps, time step, cut-off), and others such as",
1429 "NEMD parameters, which are corrected so that the net acceleration",
1431 "Eventually a binary file is produced that can serve as the sole input",
1432 "file for the MD program.[PAR]",
1434 "[THISMODULE] uses the atom names from the topology file. The atom names",
1435 "in the coordinate file (option [TT]-c[tt]) are only read to generate",
1436 "warnings when they do not match the atom names in the topology.",
1437 "Note that the atom names are irrelevant for the simulation as",
1438 "only the atom types are used for generating interaction parameters.[PAR]",
1440 "[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
1441 "etc. The preprocessor supports the following keywords::",
1444 " #ifndef VARIABLE",
1447 " #define VARIABLE",
1449 " #include \"filename\"",
1450 " #include <filename>",
1452 "The functioning of these statements in your topology may be modulated by",
1453 "using the following two flags in your [REF].mdp[ref] file::",
1455 " define = -DVARIABLE1 -DVARIABLE2",
1456 " include = -I/home/john/doe",
1458 "For further information a C-programming textbook may help you out.",
1459 "Specifying the [TT]-pp[tt] flag will get the pre-processed",
1460 "topology file written out so that you can verify its contents.[PAR]",
1462 "When using position restraints a file with restraint coordinates",
1463 "can be supplied with [TT]-r[tt], otherwise restraining will be done",
1464 "with respect to the conformation from the [TT]-c[tt] option.",
1465 "For free energy calculation the the coordinates for the B topology",
1466 "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
1467 "those of the A topology.[PAR]",
1469 "Starting coordinates can be read from trajectory with [TT]-t[tt].",
1470 "The last frame with coordinates and velocities will be read,",
1471 "unless the [TT]-time[tt] option is used. Only if this information",
1472 "is absent will the coordinates in the [TT]-c[tt] file be used.",
1473 "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
1474 "in your [REF].mdp[ref] file. An energy file can be supplied with",
1475 "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
1478 "[THISMODULE] can be used to restart simulations (preserving",
1479 "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
1480 "However, for simply changing the number of run steps to extend",
1481 "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].",
1482 "You then supply the old checkpoint file directly to [gmx-mdrun]",
1483 "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
1484 "like output frequency, then supplying the checkpoint file to",
1485 "[THISMODULE] with [TT]-t[tt] along with a new [REF].mdp[ref] file",
1486 "with [TT]-f[tt] is the recommended procedure.[PAR]",
1488 "By default, all bonded interactions which have constant energy due to",
1489 "virtual site constructions will be removed. If this constant energy is",
1490 "not zero, this will result in a shift in the total energy. All bonded",
1491 "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
1492 "all constraints for distances which will be constant anyway because",
1493 "of virtual site constructions will be removed. If any constraints remain",
1494 "which involve virtual sites, a fatal error will result.[PAR]"
1496 "To verify your run input file, please take note of all warnings",
1497 "on the screen, and correct where necessary. Do also look at the contents",
1498 "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
1499 "the input that [THISMODULE] has read. If in doubt, you can start [THISMODULE]",
1500 "with the [TT]-debug[tt] option which will give you more information",
1501 "in a file called [TT]grompp.log[tt] (along with real debug info). You",
1502 "can see the contents of the run input file with the [gmx-dump]",
1503 "program. [gmx-check] can be used to compare the contents of two",
1504 "run input files.[PAR]"
1506 "The [TT]-maxwarn[tt] option can be used to override warnings printed",
1507 "by [THISMODULE] that otherwise halt output. In some cases, warnings are",
1508 "harmless, but usually they are not. The user is advised to carefully",
1509 "interpret the output messages before attempting to bypass them with",
1515 t_molinfo *mi, *intermolecular_interactions;
1516 gpp_atomtype_t atype;
1518 int natoms, nvsite, comb, mt;
1522 real max_spacing, fudgeQQ;
1524 char fn[STRLEN], fnB[STRLEN];
1525 const char *mdparin;
1527 gmx_bool bNeedVel, bGenVel;
1528 gmx_bool have_atomnumber;
1530 t_params *gb_plist = NULL;
1531 gmx_genborn_t *born = NULL;
1533 gmx_bool bVerbose = FALSE;
1535 char warn_buf[STRLEN];
1537 t_atoms IMDatoms; /* Atoms to be operated on interactively (IMD) */
1540 { efMDP, NULL, NULL, ffREAD },
1541 { efMDP, "-po", "mdout", ffWRITE },
1542 { efSTX, "-c", NULL, ffREAD },
1543 { efSTX, "-r", NULL, ffOPTRD },
1544 { efSTX, "-rb", NULL, ffOPTRD },
1545 { efNDX, NULL, NULL, ffOPTRD },
1546 { efTOP, NULL, NULL, ffREAD },
1547 { efTOP, "-pp", "processed", ffOPTWR },
1548 { efTPR, "-o", NULL, ffWRITE },
1549 { efTRN, "-t", NULL, ffOPTRD },
1550 { efEDR, "-e", NULL, ffOPTRD },
1551 /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
1552 { efGRO, "-imd", "imdgroup", ffOPTWR },
1553 { efTRN, "-ref", "rotref", ffOPTRW }
1555 #define NFILE asize(fnm)
1557 /* Command line options */
1558 static gmx_bool bRenum = TRUE;
1559 static gmx_bool bRmVSBds = TRUE, bZero = FALSE;
1560 static int i, maxwarn = 0;
1561 static real fr_time = -1;
1563 { "-v", FALSE, etBOOL, {&bVerbose},
1564 "Be loud and noisy" },
1565 { "-time", FALSE, etREAL, {&fr_time},
1566 "Take frame at or first after this time." },
1567 { "-rmvsbds", FALSE, etBOOL, {&bRmVSBds},
1568 "Remove constant bonded interactions with virtual sites" },
1569 { "-maxwarn", FALSE, etINT, {&maxwarn},
1570 "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
1571 { "-zero", FALSE, etBOOL, {&bZero},
1572 "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
1573 { "-renum", FALSE, etBOOL, {&bRenum},
1574 "Renumber atomtypes and minimize number of atomtypes" }
1577 /* Initiate some variables */
1582 /* Parse the command line */
1583 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
1584 asize(desc), desc, 0, NULL, &oenv))
1589 wi = init_warning(TRUE, maxwarn);
1591 /* PARAMETER file processing */
1592 mdparin = opt2fn("-f", NFILE, fnm);
1593 set_warning_line(wi, mdparin, -1);
1594 get_ir(mdparin, opt2fn("-po", NFILE, fnm), ir, opts, wi);
1598 fprintf(stderr, "checking input for internal consistency...\n");
1600 check_ir(mdparin, ir, opts, wi);
1602 if (ir->ld_seed == -1)
1604 ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed();
1605 fprintf(stderr, "Setting the LD random seed to %"GMX_PRId64 "\n", ir->ld_seed);
1608 if (ir->expandedvals->lmc_seed == -1)
1610 ir->expandedvals->lmc_seed = (int)gmx_rng_make_seed();
1611 fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
1614 bNeedVel = EI_STATE_VELOCITY(ir->eI);
1615 bGenVel = (bNeedVel && opts->bGenVel);
1616 if (bGenVel && ir->bContinuation)
1619 "Generating velocities is inconsistent with attempting "
1620 "to continue a previous run. Choose only one of "
1621 "gen-vel = yes and continuation = yes.");
1622 warning_error(wi, warn_buf);
1628 atype = init_atomtype();
1631 pr_symtab(debug, 0, "Just opened", &sys->symtab);
1634 strcpy(fn, ftp2fn(efTOP, NFILE, fnm));
1635 if (!gmx_fexist(fn))
1637 gmx_fatal(FARGS, "%s does not exist", fn);
1640 new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
1641 opts, ir, bZero, bGenVel, bVerbose, state,
1642 atype, sys, &nmi, &mi, &intermolecular_interactions,
1643 plist, &comb, &reppow, &fudgeQQ,
1649 pr_symtab(debug, 0, "After new_status", &sys->symtab);
1653 /* set parameters for virtual site construction (not for vsiten) */
1654 for (mt = 0; mt < sys->nmoltype; mt++)
1657 set_vsites(bVerbose, &sys->moltype[mt].atoms, atype, mi[mt].plist);
1659 /* now throw away all obsolete bonds, angles and dihedrals: */
1660 /* note: constraints are ALWAYS removed */
1663 for (mt = 0; mt < sys->nmoltype; mt++)
1665 clean_vsite_bondeds(mi[mt].plist, sys->moltype[mt].atoms.nr, bRmVSBds);
1669 if (nvsite && ir->eI == eiNM)
1671 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");
1674 if (ir->cutoff_scheme == ecutsVERLET)
1676 fprintf(stderr, "Removing all charge groups because cutoff-scheme=%s\n",
1677 ecutscheme_names[ir->cutoff_scheme]);
1679 /* Remove all charge groups */
1680 gmx_mtop_remove_chargegroups(sys);
1683 if (count_constraints(sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
1685 if (ir->eI == eiCG || ir->eI == eiLBFGS)
1687 sprintf(warn_buf, "Can not do %s with %s, use %s",
1688 EI(ir->eI), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1689 warning_error(wi, warn_buf);
1691 if (ir->bPeriodicMols)
1693 sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
1694 econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1695 warning_error(wi, warn_buf);
1699 if (EI_SD (ir->eI) && ir->etc != etcNO)
1701 warning_note(wi, "Temperature coupling is ignored with SD integrators.");
1704 /* If we are doing QM/MM, check that we got the atom numbers */
1705 have_atomnumber = TRUE;
1706 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1708 have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
1710 if (!have_atomnumber && ir->bQMMM)
1714 "It appears as if you are trying to run a QM/MM calculation, but the force\n"
1715 "field you are using does not contain atom numbers fields. This is an\n"
1716 "optional field (introduced in GROMACS 3.3) for general runs, but mandatory\n"
1717 "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
1718 "an integer just before the mass column in ffXXXnb.itp.\n"
1719 "NB: United atoms have the same atom numbers as normal ones.\n\n");
1724 if ((ir->adress->const_wf > 1) || (ir->adress->const_wf < 0))
1726 warning_error(wi, "AdResS contant weighting function should be between 0 and 1\n\n");
1728 /** TODO check size of ex+hy width against box size */
1731 /* Check for errors in the input now, since they might cause problems
1732 * during processing further down.
1734 check_warning_error(wi, FARGS);
1736 if (opt2bSet("-r", NFILE, fnm))
1738 sprintf(fn, "%s", opt2fn("-r", NFILE, fnm));
1742 sprintf(fn, "%s", opt2fn("-c", NFILE, fnm));
1744 if (opt2bSet("-rb", NFILE, fnm))
1746 sprintf(fnB, "%s", opt2fn("-rb", NFILE, fnm));
1753 if (nint_ftype(sys, mi, F_POSRES) > 0 || nint_ftype(sys, mi, F_FBPOSRES) > 0)
1757 fprintf(stderr, "Reading position restraint coords from %s", fn);
1758 if (strcmp(fn, fnB) == 0)
1760 fprintf(stderr, "\n");
1764 fprintf(stderr, " and %s\n", fnB);
1767 gen_posres(sys, mi, fn, fnB,
1768 ir->refcoord_scaling, ir->ePBC,
1769 ir->posres_com, ir->posres_comB,
1773 /* If we are using CMAP, setup the pre-interpolation grid */
1774 if (plist[F_CMAP].ncmap > 0)
1776 init_cmap_grid(&sys->ffparams.cmap_grid, plist[F_CMAP].nc, plist[F_CMAP].grid_spacing);
1777 setup_cmap(plist[F_CMAP].grid_spacing, plist[F_CMAP].nc, plist[F_CMAP].cmap, &sys->ffparams.cmap_grid);
1780 set_wall_atomtype(atype, opts, ir, wi);
1783 renum_atype(plist, sys, ir->wall_atomtype, atype, bVerbose);
1784 ntype = get_atomtype_ntypes(atype);
1787 if (ir->implicit_solvent != eisNO)
1789 /* Now we have renumbered the atom types, we can check the GBSA params */
1790 check_gbsa_params(atype);
1792 /* Check that all atoms that have charge and/or LJ-parameters also have
1793 * sensible GB-parameters
1795 check_gbsa_params_charged(sys, atype);
1798 /* PELA: Copy the atomtype data to the topology atomtype list */
1799 copy_atomtype_atomtypes(atype, &(sys->atomtypes));
1803 pr_symtab(debug, 0, "After renum_atype", &sys->symtab);
1808 fprintf(stderr, "converting bonded parameters...\n");
1811 ntype = get_atomtype_ntypes(atype);
1812 convert_params(ntype, plist, mi, intermolecular_interactions,
1813 comb, reppow, fudgeQQ, sys);
1817 pr_symtab(debug, 0, "After convert_params", &sys->symtab);
1820 /* set ptype to VSite for virtual sites */
1821 for (mt = 0; mt < sys->nmoltype; mt++)
1823 set_vsites_ptype(FALSE, &sys->moltype[mt]);
1827 pr_symtab(debug, 0, "After virtual sites", &sys->symtab);
1829 /* Check velocity for virtual sites and shells */
1832 check_vel(sys, state->v);
1835 /* check for shells and inpurecs */
1836 check_shells_inputrec(sys, ir, wi);
1841 for (i = 0; i < sys->nmoltype; i++)
1843 check_cg_sizes(ftp2fn(efTOP, NFILE, fnm), &sys->moltype[i].cgs, wi);
1846 if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
1848 check_bonds_timestep(sys, ir->delta_t, wi);
1851 if (EI_ENERGY_MINIMIZATION(ir->eI) && 0 == ir->nsteps)
1853 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.");
1856 check_warning_error(wi, FARGS);
1860 fprintf(stderr, "initialising group options...\n");
1862 do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
1864 bGenVel ? state->v : NULL,
1867 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 &&
1870 if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
1874 if (EI_MD(ir->eI) && ir->etc == etcNO)
1878 buffer_temp = opts->tempi;
1882 buffer_temp = calc_temp(sys, ir, state->v);
1884 if (buffer_temp > 0)
1886 sprintf(warn_buf, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp);
1887 warning_note(wi, warn_buf);
1891 sprintf(warn_buf, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
1892 (int)(verlet_buffer_ratio_NVE_T0*100 + 0.5));
1893 warning_note(wi, warn_buf);
1898 buffer_temp = get_max_reference_temp(ir, wi);
1901 if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
1903 /* NVE with initial T=0: we add a fixed ratio to rlist.
1904 * Since we don't actually use verletbuf_tol, we set it to -1
1905 * so it can't be misused later.
1907 ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
1908 ir->verletbuf_tol = -1;
1912 /* We warn for NVE simulations with >1(.1)% drift tolerance */
1913 const real drift_tol = 0.01;
1916 /* We use 2 DOF per atom = 2kT pot+kin energy, to be on
1917 * the safe side with constraints (without constraints: 3 DOF).
1919 ener_runtime = 2*BOLTZ*buffer_temp/(ir->nsteps*ir->delta_t);
1921 if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 &&
1923 ir->verletbuf_tol > 1.1*drift_tol*ener_runtime)
1925 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.",
1926 ir->verletbuf_tol, ir->nsteps*ir->delta_t,
1927 (int)(ir->verletbuf_tol/ener_runtime*100 + 0.5),
1928 (int)(100*drift_tol + 0.5),
1929 drift_tol*ener_runtime);
1930 warning_note(wi, warn_buf);
1933 set_verlet_buffer(sys, ir, buffer_temp, state->box, wi);
1938 /* Init the temperature coupling state */
1939 init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
1943 fprintf(stderr, "Checking consistency between energy and charge groups...\n");
1945 check_eg_vs_cg(sys);
1949 pr_symtab(debug, 0, "After index", &sys->symtab);
1952 triple_check(mdparin, ir, sys, wi);
1953 close_symtab(&sys->symtab);
1956 pr_symtab(debug, 0, "After close", &sys->symtab);
1959 /* make exclusions between QM atoms */
1962 if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
1964 gmx_fatal(FARGS, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
1968 generate_qmexcl(sys, ir, wi);
1972 if (ftp2bSet(efTRN, NFILE, fnm))
1976 fprintf(stderr, "getting data from old trajectory ...\n");
1978 cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
1979 bNeedVel, bGenVel, fr_time, ir, state, sys, oenv);
1982 if (ir->ePBC == epbcXY && ir->nwall != 2)
1984 clear_rvec(state->box[ZZ]);
1987 if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
1989 set_warning_line(wi, mdparin, -1);
1990 check_chargegroup_radii(sys, ir, state->x, wi);
1993 if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1995 /* Calculate the optimal grid dimensions */
1996 copy_mat(state->box, box);
1997 if (ir->ePBC == epbcXY && ir->nwall == 2)
1999 svmul(ir->wall_ewald_zfac, box[ZZ], box[ZZ]);
2001 if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
2003 /* Mark fourier_spacing as not used */
2004 ir->fourier_spacing = 0;
2006 else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
2008 set_warning_line(wi, mdparin, -1);
2009 warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
2011 max_spacing = calc_grid(stdout, box, ir->fourier_spacing,
2012 &(ir->nkx), &(ir->nky), &(ir->nkz));
2015 /* MRS: eventually figure out better logic for initializing the fep
2016 values that makes declaring the lambda and declaring the state not
2017 potentially conflict if not handled correctly. */
2018 if (ir->efep != efepNO)
2020 state->fep_state = ir->fepvals->init_fep_state;
2021 for (i = 0; i < efptNR; i++)
2023 /* init_lambda trumps state definitions*/
2024 if (ir->fepvals->init_lambda >= 0)
2026 state->lambda[i] = ir->fepvals->init_lambda;
2030 if (ir->fepvals->all_lambda[i] == NULL)
2032 gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
2036 state->lambda[i] = ir->fepvals->all_lambda[i][state->fep_state];
2044 set_pull_init(ir, sys, state->x, state->box, state->lambda[efptMASS], oenv);
2049 set_reference_positions(ir->rot, state->x, state->box,
2050 opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
2054 /* reset_multinr(sys); */
2056 if (EEL_PME(ir->coulombtype))
2058 float ratio = pme_load_estimate(sys, ir, state->box);
2059 fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
2060 /* With free energy we might need to do PME both for the A and B state
2061 * charges. This will double the cost, but the optimal performance will
2062 * then probably be at a slightly larger cut-off and grid spacing.
2064 if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
2065 (ir->efep != efepNO && ratio > 2.0/3.0))
2068 "The optimal PME mesh load for parallel simulations is below 0.5\n"
2069 "and for highly parallel simulations between 0.25 and 0.33,\n"
2070 "for higher performance, increase the cut-off and the PME grid spacing.\n");
2071 if (ir->efep != efepNO)
2074 "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
2080 char warn_buf[STRLEN];
2081 double cio = compute_io(ir, sys->natoms, &sys->groups, F_NRE, 1);
2082 sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
2085 set_warning_line(wi, mdparin, -1);
2086 warning_note(wi, warn_buf);
2090 printf("%s\n", warn_buf);
2096 fprintf(stderr, "writing run input file...\n");
2099 done_warning(wi, FARGS);
2100 write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, state, sys);
2102 /* Output IMD group, if bIMD is TRUE */
2103 write_IMDgroup_to_file(ir->bIMD, ir, state, sys, NFILE, fnm);
2107 done_atomtype(atype);
2108 done_mtop(sys, TRUE);
2109 done_inputrec_strings();