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49 #include <sys/types.h>
51 #include "gromacs/commandline/pargs.h"
52 #include "gromacs/fileio/confio.h"
53 #include "gromacs/fileio/enxio.h"
54 #include "gromacs/fileio/tpxio.h"
55 #include "gromacs/fileio/trx.h"
56 #include "gromacs/fileio/trxio.h"
57 #include "gromacs/gmxlib/calcgrid.h"
58 #include "gromacs/gmxlib/splitter.h"
59 #include "gromacs/gmxlib/warninp.h"
60 #include "gromacs/gmxpreprocess/add_par.h"
61 #include "gromacs/gmxpreprocess/convparm.h"
62 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
63 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
64 #include "gromacs/gmxpreprocess/grompp-impl.h"
65 #include "gromacs/gmxpreprocess/notset.h"
66 #include "gromacs/gmxpreprocess/readir.h"
67 #include "gromacs/gmxpreprocess/tomorse.h"
68 #include "gromacs/gmxpreprocess/topio.h"
69 #include "gromacs/gmxpreprocess/toputil.h"
70 #include "gromacs/gmxpreprocess/vsite_parm.h"
71 #include "gromacs/imd/imd.h"
72 #include "gromacs/legacyheaders/genborn.h"
73 #include "gromacs/legacyheaders/names.h"
74 #include "gromacs/legacyheaders/txtdump.h"
75 #include "gromacs/legacyheaders/types/ifunc.h"
76 #include "gromacs/math/vec.h"
77 #include "gromacs/mdlib/calc_verletbuf.h"
78 #include "gromacs/mdlib/compute_io.h"
79 #include "gromacs/mdlib/perf_est.h"
80 #include "gromacs/pbcutil/boxutilities.h"
81 #include "gromacs/pbcutil/pbc.h"
82 #include "gromacs/random/random.h"
83 #include "gromacs/topology/mtop_util.h"
84 #include "gromacs/topology/symtab.h"
85 #include "gromacs/topology/topology.h"
86 #include "gromacs/utility/arraysize.h"
87 #include "gromacs/utility/cstringutil.h"
88 #include "gromacs/utility/fatalerror.h"
89 #include "gromacs/utility/futil.h"
90 #include "gromacs/utility/gmxassert.h"
91 #include "gromacs/utility/smalloc.h"
92 #include "gromacs/utility/snprintf.h"
94 static int rm_interactions(int ifunc
, int nrmols
, t_molinfo mols
[])
99 /* For all the molecule types */
100 for (i
= 0; i
< nrmols
; i
++)
102 n
+= mols
[i
].plist
[ifunc
].nr
;
103 mols
[i
].plist
[ifunc
].nr
= 0;
108 static int check_atom_names(const char *fn1
, const char *fn2
,
109 gmx_mtop_t
*mtop
, t_atoms
*at
)
111 int mb
, m
, i
, j
, nmismatch
;
113 #define MAXMISMATCH 20
115 if (mtop
->natoms
!= at
->nr
)
117 gmx_incons("comparing atom names");
122 for (mb
= 0; mb
< mtop
->nmolblock
; mb
++)
124 tat
= &mtop
->moltype
[mtop
->molblock
[mb
].type
].atoms
;
125 for (m
= 0; m
< mtop
->molblock
[mb
].nmol
; m
++)
127 for (j
= 0; j
< tat
->nr
; j
++)
129 if (strcmp( *(tat
->atomname
[j
]), *(at
->atomname
[i
]) ) != 0)
131 if (nmismatch
< MAXMISMATCH
)
134 "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
135 i
+1, fn1
, fn2
, *(tat
->atomname
[j
]), *(at
->atomname
[i
]));
137 else if (nmismatch
== MAXMISMATCH
)
139 fprintf(stderr
, "(more than %d non-matching atom names)\n", MAXMISMATCH
);
151 static void check_eg_vs_cg(gmx_mtop_t
*mtop
)
153 int astart
, mb
, m
, cg
, j
, firstj
;
154 unsigned char firsteg
, eg
;
157 /* Go through all the charge groups and make sure all their
158 * atoms are in the same energy group.
162 for (mb
= 0; mb
< mtop
->nmolblock
; mb
++)
164 molt
= &mtop
->moltype
[mtop
->molblock
[mb
].type
];
165 for (m
= 0; m
< mtop
->molblock
[mb
].nmol
; m
++)
167 for (cg
= 0; cg
< molt
->cgs
.nr
; cg
++)
169 /* Get the energy group of the first atom in this charge group */
170 firstj
= astart
+ molt
->cgs
.index
[cg
];
171 firsteg
= ggrpnr(&mtop
->groups
, egcENER
, firstj
);
172 for (j
= molt
->cgs
.index
[cg
]+1; j
< molt
->cgs
.index
[cg
+1]; j
++)
174 eg
= ggrpnr(&mtop
->groups
, egcENER
, astart
+j
);
177 gmx_fatal(FARGS
, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
178 firstj
+1, astart
+j
+1, cg
+1, *molt
->name
);
182 astart
+= molt
->atoms
.nr
;
187 static void check_cg_sizes(const char *topfn
, t_block
*cgs
, warninp_t wi
)
190 char warn_buf
[STRLEN
];
193 for (cg
= 0; cg
< cgs
->nr
; cg
++)
195 maxsize
= std::max(maxsize
, cgs
->index
[cg
+1]-cgs
->index
[cg
]);
198 if (maxsize
> MAX_CHARGEGROUP_SIZE
)
200 gmx_fatal(FARGS
, "The largest charge group contains %d atoms. The maximum is %d.", maxsize
, MAX_CHARGEGROUP_SIZE
);
202 else if (maxsize
> 10)
204 set_warning_line(wi
, topfn
, -1);
206 "The largest charge group contains %d atoms.\n"
207 "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"
208 "For efficiency and accuracy, charge group should consist of a few atoms.\n"
209 "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
211 warning_note(wi
, warn_buf
);
215 static void check_bonds_timestep(gmx_mtop_t
*mtop
, double dt
, warninp_t wi
)
217 /* This check is not intended to ensure accurate integration,
218 * rather it is to signal mistakes in the mdp settings.
219 * A common mistake is to forget to turn on constraints
220 * for MD after energy minimization with flexible bonds.
221 * This check can also detect too large time steps for flexible water
222 * models, but such errors will often be masked by the constraints
223 * mdp options, which turns flexible water into water with bond constraints,
224 * but without an angle constraint. Unfortunately such incorrect use
225 * of water models can not easily be detected without checking
226 * for specific model names.
228 * The stability limit of leap-frog or velocity verlet is 4.44 steps
229 * per oscillational period.
230 * But accurate bonds distributions are lost far before that limit.
231 * To allow relatively common schemes (although not common with Gromacs)
232 * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
233 * we set the note limit to 10.
235 int min_steps_warn
= 5;
236 int min_steps_note
= 10;
239 gmx_moltype_t
*moltype
, *w_moltype
;
241 t_ilist
*ilist
, *ilb
, *ilc
, *ils
;
243 int i
, a1
, a2
, w_a1
, w_a2
, j
;
244 real twopi2
, limit2
, fc
, re
, m1
, m2
, period2
, w_period2
;
245 gmx_bool bFound
, bWater
, bWarn
;
246 char warn_buf
[STRLEN
];
248 ip
= mtop
->ffparams
.iparams
;
250 twopi2
= sqr(2*M_PI
);
252 limit2
= sqr(min_steps_note
*dt
);
258 for (molt
= 0; molt
< mtop
->nmoltype
; molt
++)
260 moltype
= &mtop
->moltype
[molt
];
261 atom
= moltype
->atoms
.atom
;
262 ilist
= moltype
->ilist
;
263 ilc
= &ilist
[F_CONSTR
];
264 ils
= &ilist
[F_SETTLE
];
265 for (ftype
= 0; ftype
< F_NRE
; ftype
++)
267 if (!(ftype
== F_BONDS
|| ftype
== F_G96BONDS
|| ftype
== F_HARMONIC
))
273 for (i
= 0; i
< ilb
->nr
; i
+= 3)
275 fc
= ip
[ilb
->iatoms
[i
]].harmonic
.krA
;
276 re
= ip
[ilb
->iatoms
[i
]].harmonic
.rA
;
277 if (ftype
== F_G96BONDS
)
279 /* Convert squared sqaure fc to harmonic fc */
282 a1
= ilb
->iatoms
[i
+1];
283 a2
= ilb
->iatoms
[i
+2];
286 if (fc
> 0 && m1
> 0 && m2
> 0)
288 period2
= twopi2
*m1
*m2
/((m1
+ m2
)*fc
);
292 period2
= GMX_FLOAT_MAX
;
296 fprintf(debug
, "fc %g m1 %g m2 %g period %g\n",
297 fc
, m1
, m2
, std::sqrt(period2
));
299 if (period2
< limit2
)
302 for (j
= 0; j
< ilc
->nr
; j
+= 3)
304 if ((ilc
->iatoms
[j
+1] == a1
&& ilc
->iatoms
[j
+2] == a2
) ||
305 (ilc
->iatoms
[j
+1] == a2
&& ilc
->iatoms
[j
+2] == a1
))
310 for (j
= 0; j
< ils
->nr
; j
+= 4)
312 if ((a1
== ils
->iatoms
[j
+1] || a1
== ils
->iatoms
[j
+2] || a1
== ils
->iatoms
[j
+3]) &&
313 (a2
== ils
->iatoms
[j
+1] || a2
== ils
->iatoms
[j
+2] || a2
== ils
->iatoms
[j
+3]))
319 (w_moltype
== NULL
|| period2
< w_period2
))
331 if (w_moltype
!= NULL
)
333 bWarn
= (w_period2
< sqr(min_steps_warn
*dt
));
334 /* A check that would recognize most water models */
335 bWater
= ((*w_moltype
->atoms
.atomname
[0])[0] == 'O' &&
336 w_moltype
->atoms
.nr
<= 5);
337 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"
340 w_a1
+1, *w_moltype
->atoms
.atomname
[w_a1
],
341 w_a2
+1, *w_moltype
->atoms
.atomname
[w_a2
],
342 std::sqrt(w_period2
), bWarn
? min_steps_warn
: min_steps_note
, dt
,
344 "Maybe you asked for fexible water." :
345 "Maybe you forgot to change the constraints mdp option.");
348 warning(wi
, warn_buf
);
352 warning_note(wi
, warn_buf
);
357 static void check_vel(gmx_mtop_t
*mtop
, rvec v
[])
359 gmx_mtop_atomloop_all_t aloop
;
363 aloop
= gmx_mtop_atomloop_all_init(mtop
);
364 while (gmx_mtop_atomloop_all_next(aloop
, &a
, &atom
))
366 if (atom
->ptype
== eptShell
||
367 atom
->ptype
== eptBond
||
368 atom
->ptype
== eptVSite
)
375 static void check_shells_inputrec(gmx_mtop_t
*mtop
,
379 gmx_mtop_atomloop_all_t aloop
;
382 char warn_buf
[STRLEN
];
384 aloop
= gmx_mtop_atomloop_all_init(mtop
);
385 while (gmx_mtop_atomloop_all_next(aloop
, &a
, &atom
))
387 if (atom
->ptype
== eptShell
||
388 atom
->ptype
== eptBond
)
393 if (IR_TWINRANGE(*ir
) && (nshells
> 0))
395 snprintf(warn_buf
, STRLEN
,
396 "The combination of using shells and a twin-range cut-off is not supported");
397 warning_error(wi
, warn_buf
);
399 if ((nshells
> 0) && (ir
->nstcalcenergy
!= 1))
401 set_warning_line(wi
, "unknown", -1);
402 snprintf(warn_buf
, STRLEN
,
403 "There are %d shells, changing nstcalcenergy from %d to 1",
404 nshells
, ir
->nstcalcenergy
);
405 ir
->nstcalcenergy
= 1;
406 warning(wi
, warn_buf
);
410 /* TODO Decide whether this function can be consolidated with
411 * gmx_mtop_ftype_count */
412 static gmx_bool
nint_ftype(gmx_mtop_t
*mtop
, t_molinfo
*mi
, int ftype
)
417 for (mb
= 0; mb
< mtop
->nmolblock
; mb
++)
419 nint
+= mtop
->molblock
[mb
].nmol
*mi
[mtop
->molblock
[mb
].type
].plist
[ftype
].nr
;
425 /* This routine reorders the molecule type array
426 * in the order of use in the molblocks,
427 * unused molecule types are deleted.
429 static void renumber_moltypes(gmx_mtop_t
*sys
,
430 int *nmolinfo
, t_molinfo
**molinfo
)
432 int *order
, norder
, i
;
436 snew(order
, *nmolinfo
);
438 for (mb
= 0; mb
< sys
->nmolblock
; mb
++)
440 for (i
= 0; i
< norder
; i
++)
442 if (order
[i
] == sys
->molblock
[mb
].type
)
449 /* This type did not occur yet, add it */
450 order
[norder
] = sys
->molblock
[mb
].type
;
451 /* Renumber the moltype in the topology */
454 sys
->molblock
[mb
].type
= i
;
457 /* We still need to reorder the molinfo structs */
459 for (mi
= 0; mi
< *nmolinfo
; mi
++)
461 for (i
= 0; i
< norder
; i
++)
470 done_mi(&(*molinfo
)[mi
]);
474 minew
[i
] = (*molinfo
)[mi
];
483 static void molinfo2mtop(int nmi
, t_molinfo
*mi
, gmx_mtop_t
*mtop
)
488 mtop
->nmoltype
= nmi
;
489 snew(mtop
->moltype
, nmi
);
490 for (m
= 0; m
< nmi
; m
++)
492 molt
= &mtop
->moltype
[m
];
493 molt
->name
= mi
[m
].name
;
494 molt
->atoms
= mi
[m
].atoms
;
495 /* ilists are copied later */
496 molt
->cgs
= mi
[m
].cgs
;
497 molt
->excls
= mi
[m
].excls
;
502 new_status(const char *topfile
, const char *topppfile
, const char *confin
,
503 t_gromppopts
*opts
, t_inputrec
*ir
, gmx_bool bZero
,
504 gmx_bool bGenVel
, gmx_bool bVerbose
, t_state
*state
,
505 gpp_atomtype_t atype
, gmx_mtop_t
*sys
,
506 int *nmi
, t_molinfo
**mi
, t_molinfo
**intermolecular_interactions
,
508 int *comb
, double *reppow
, real
*fudgeQQ
,
512 t_molinfo
*molinfo
= NULL
;
514 gmx_molblock_t
*molblock
, *molbs
;
515 int mb
, i
, nrmols
, nmismatch
;
517 gmx_bool bGB
= FALSE
;
518 char warn_buf
[STRLEN
];
522 /* Set gmx_boolean for GB */
523 if (ir
->implicit_solvent
)
528 /* TOPOLOGY processing */
529 sys
->name
= do_top(bVerbose
, topfile
, topppfile
, opts
, bZero
, &(sys
->symtab
),
530 plist
, comb
, reppow
, fudgeQQ
,
531 atype
, &nrmols
, &molinfo
, intermolecular_interactions
,
533 &nmolblock
, &molblock
, bGB
,
537 snew(sys
->molblock
, nmolblock
);
540 for (mb
= 0; mb
< nmolblock
; mb
++)
542 if (sys
->nmolblock
> 0 &&
543 molblock
[mb
].type
== sys
->molblock
[sys
->nmolblock
-1].type
)
545 /* Merge consecutive blocks with the same molecule type */
546 sys
->molblock
[sys
->nmolblock
-1].nmol
+= molblock
[mb
].nmol
;
547 sys
->natoms
+= molblock
[mb
].nmol
*sys
->molblock
[sys
->nmolblock
-1].natoms_mol
;
549 else if (molblock
[mb
].nmol
> 0)
551 /* Add a new molblock to the topology */
552 molbs
= &sys
->molblock
[sys
->nmolblock
];
553 *molbs
= molblock
[mb
];
554 molbs
->natoms_mol
= molinfo
[molbs
->type
].atoms
.nr
;
555 molbs
->nposres_xA
= 0;
556 molbs
->nposres_xB
= 0;
557 sys
->natoms
+= molbs
->nmol
*molbs
->natoms_mol
;
561 if (sys
->nmolblock
== 0)
563 gmx_fatal(FARGS
, "No molecules were defined in the system");
566 renumber_moltypes(sys
, &nrmols
, &molinfo
);
570 convert_harmonics(nrmols
, molinfo
, atype
);
573 if (ir
->eDisre
== edrNone
)
575 i
= rm_interactions(F_DISRES
, nrmols
, molinfo
);
578 set_warning_line(wi
, "unknown", -1);
579 sprintf(warn_buf
, "disre = no, removed %d distance restraints", i
);
580 warning_note(wi
, warn_buf
);
583 if (opts
->bOrire
== FALSE
)
585 i
= rm_interactions(F_ORIRES
, nrmols
, molinfo
);
588 set_warning_line(wi
, "unknown", -1);
589 sprintf(warn_buf
, "orire = no, removed %d orientation restraints", i
);
590 warning_note(wi
, warn_buf
);
594 /* Copy structures from msys to sys */
595 molinfo2mtop(nrmols
, molinfo
, sys
);
597 gmx_mtop_finalize(sys
);
599 /* COORDINATE file processing */
602 fprintf(stderr
, "processing coordinates...\n");
607 init_state(state
, 0, 0, 0, 0, 0);
608 read_tps_conf(confin
, conftop
, NULL
, &state
->x
, &state
->v
, state
->box
, FALSE
);
609 state
->natoms
= state
->nalloc
= conftop
->atoms
.nr
;
610 if (state
->natoms
!= sys
->natoms
)
612 gmx_fatal(FARGS
, "number of coordinates in coordinate file (%s, %d)\n"
613 " does not match topology (%s, %d)",
614 confin
, state
->natoms
, topfile
, sys
->natoms
);
616 /* This call fixes the box shape for runs with pressure scaling */
617 set_box_rel(ir
, state
);
619 nmismatch
= check_atom_names(topfile
, confin
, sys
, &conftop
->atoms
);
625 sprintf(buf
, "%d non-matching atom name%s\n"
626 "atom names from %s will be used\n"
627 "atom names from %s will be ignored\n",
628 nmismatch
, (nmismatch
== 1) ? "" : "s", topfile
, confin
);
632 /* Do more checks, mostly related to constraints */
635 fprintf(stderr
, "double-checking input for internal consistency...\n");
638 int bHasNormalConstraints
= 0 < (nint_ftype(sys
, molinfo
, F_CONSTR
) +
639 nint_ftype(sys
, molinfo
, F_CONSTRNC
));
640 int bHasAnyConstraints
= bHasNormalConstraints
|| 0 < nint_ftype(sys
, molinfo
, F_SETTLE
);
641 double_check(ir
, state
->box
,
642 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 gmx_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
,
818 int natoms
, npbcdim
= 0;
819 char warn_buf
[STRLEN
];
820 int a
, i
, ai
, j
, k
, mb
, nat_molb
;
821 gmx_molblock_t
*molb
;
826 read_tps_conf(fn
, top
, NULL
, &x
, &v
, box
, FALSE
);
827 natoms
= top
->atoms
.nr
;
830 if (natoms
!= mtop
->natoms
)
832 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
, std::min(mtop
->natoms
, natoms
), fn
);
833 warning(wi
, warn_buf
);
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 GMX_ASSERT(npbcdim
<= DIM
, "Only DIM dimensions can have PBC");
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
];
988 static void gen_posres(gmx_mtop_t
*mtop
, t_molinfo
*mi
,
989 char *fnA
, char *fnB
,
990 int rc_scaling
, int ePBC
,
994 read_posres (mtop
, mi
, FALSE
, fnA
, rc_scaling
, ePBC
, com
, wi
);
995 /* It is safer to simply read the b-state posres rather than trying
996 * to be smart and copy the positions.
998 read_posres(mtop
, mi
, TRUE
, fnB
, rc_scaling
, ePBC
, comB
, wi
);
1001 static void set_wall_atomtype(gpp_atomtype_t at
, t_gromppopts
*opts
,
1002 t_inputrec
*ir
, warninp_t wi
)
1005 char warn_buf
[STRLEN
];
1009 fprintf(stderr
, "Searching the wall atom type(s)\n");
1011 for (i
= 0; i
< ir
->nwall
; i
++)
1013 ir
->wall_atomtype
[i
] = get_atomtype_type(opts
->wall_atomtype
[i
], at
);
1014 if (ir
->wall_atomtype
[i
] == NOTSET
)
1016 sprintf(warn_buf
, "Specified wall atom type %s is not defined", opts
->wall_atomtype
[i
]);
1017 warning_error(wi
, warn_buf
);
1022 static int nrdf_internal(t_atoms
*atoms
)
1027 for (i
= 0; i
< atoms
->nr
; i
++)
1029 /* Vsite ptype might not be set here yet, so also check the mass */
1030 if ((atoms
->atom
[i
].ptype
== eptAtom
||
1031 atoms
->atom
[i
].ptype
== eptNucleus
)
1032 && atoms
->atom
[i
].m
> 0)
1039 case 0: nrdf
= 0; break;
1040 case 1: nrdf
= 0; break;
1041 case 2: nrdf
= 1; break;
1042 default: nrdf
= nmass
*3 - 6; break;
1049 spline1d( double dx
,
1061 for (i
= 1; i
< n
-1; i
++)
1063 p
= 0.5*y2
[i
-1]+2.0;
1065 q
= (y
[i
+1]-2.0*y
[i
]+y
[i
-1])/dx
;
1066 u
[i
] = (3.0*q
/dx
-0.5*u
[i
-1])/p
;
1071 for (i
= n
-2; i
>= 0; i
--)
1073 y2
[i
] = y2
[i
]*y2
[i
+1]+u
[i
];
1079 interpolate1d( double xmin
,
1090 ix
= static_cast<int>((x
-xmin
)/dx
);
1092 a
= (xmin
+(ix
+1)*dx
-x
)/dx
;
1093 b
= (x
-xmin
-ix
*dx
)/dx
;
1095 *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;
1096 *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];
1101 setup_cmap (int grid_spacing
,
1104 gmx_cmap_t
* cmap_grid
)
1106 double *tmp_u
, *tmp_u2
, *tmp_yy
, *tmp_y1
, *tmp_t2
, *tmp_grid
;
1108 int i
, j
, k
, ii
, jj
, kk
, idx
;
1110 double dx
, xmin
, v
, v1
, v2
, v12
;
1113 snew(tmp_u
, 2*grid_spacing
);
1114 snew(tmp_u2
, 2*grid_spacing
);
1115 snew(tmp_yy
, 2*grid_spacing
);
1116 snew(tmp_y1
, 2*grid_spacing
);
1117 snew(tmp_t2
, 2*grid_spacing
*2*grid_spacing
);
1118 snew(tmp_grid
, 2*grid_spacing
*2*grid_spacing
);
1120 dx
= 360.0/grid_spacing
;
1121 xmin
= -180.0-dx
*grid_spacing
/2;
1123 for (kk
= 0; kk
< nc
; kk
++)
1125 /* Compute an offset depending on which cmap we are using
1126 * Offset will be the map number multiplied with the
1127 * grid_spacing * grid_spacing * 2
1129 offset
= kk
* grid_spacing
* grid_spacing
* 2;
1131 for (i
= 0; i
< 2*grid_spacing
; i
++)
1133 ii
= (i
+grid_spacing
-grid_spacing
/2)%grid_spacing
;
1135 for (j
= 0; j
< 2*grid_spacing
; j
++)
1137 jj
= (j
+grid_spacing
-grid_spacing
/2)%grid_spacing
;
1138 tmp_grid
[i
*grid_spacing
*2+j
] = grid
[offset
+ii
*grid_spacing
+jj
];
1142 for (i
= 0; i
< 2*grid_spacing
; i
++)
1144 spline1d(dx
, &(tmp_grid
[2*grid_spacing
*i
]), 2*grid_spacing
, tmp_u
, &(tmp_t2
[2*grid_spacing
*i
]));
1147 for (i
= grid_spacing
/2; i
< grid_spacing
+grid_spacing
/2; i
++)
1149 ii
= i
-grid_spacing
/2;
1152 for (j
= grid_spacing
/2; j
< grid_spacing
+grid_spacing
/2; j
++)
1154 jj
= j
-grid_spacing
/2;
1157 for (k
= 0; k
< 2*grid_spacing
; k
++)
1159 interpolate1d(xmin
, dx
, &(tmp_grid
[2*grid_spacing
*k
]),
1160 &(tmp_t2
[2*grid_spacing
*k
]), psi
, &tmp_yy
[k
], &tmp_y1
[k
]);
1163 spline1d(dx
, tmp_yy
, 2*grid_spacing
, tmp_u
, tmp_u2
);
1164 interpolate1d(xmin
, dx
, tmp_yy
, tmp_u2
, phi
, &v
, &v1
);
1165 spline1d(dx
, tmp_y1
, 2*grid_spacing
, tmp_u
, tmp_u2
);
1166 interpolate1d(xmin
, dx
, tmp_y1
, tmp_u2
, phi
, &v2
, &v12
);
1168 idx
= ii
*grid_spacing
+jj
;
1169 cmap_grid
->cmapdata
[kk
].cmap
[idx
*4] = grid
[offset
+ii
*grid_spacing
+jj
];
1170 cmap_grid
->cmapdata
[kk
].cmap
[idx
*4+1] = v1
;
1171 cmap_grid
->cmapdata
[kk
].cmap
[idx
*4+2] = v2
;
1172 cmap_grid
->cmapdata
[kk
].cmap
[idx
*4+3] = v12
;
1178 void init_cmap_grid(gmx_cmap_t
*cmap_grid
, int ngrid
, int grid_spacing
)
1182 cmap_grid
->ngrid
= ngrid
;
1183 cmap_grid
->grid_spacing
= grid_spacing
;
1184 nelem
= cmap_grid
->grid_spacing
*cmap_grid
->grid_spacing
;
1186 snew(cmap_grid
->cmapdata
, ngrid
);
1188 for (i
= 0; i
< cmap_grid
->ngrid
; i
++)
1190 snew(cmap_grid
->cmapdata
[i
].cmap
, 4*nelem
);
1195 static int count_constraints(gmx_mtop_t
*mtop
, t_molinfo
*mi
, warninp_t wi
)
1197 int count
, count_mol
, i
, mb
;
1198 gmx_molblock_t
*molb
;
1203 for (mb
= 0; mb
< mtop
->nmolblock
; mb
++)
1206 molb
= &mtop
->molblock
[mb
];
1207 plist
= mi
[molb
->type
].plist
;
1209 for (i
= 0; i
< F_NRE
; i
++)
1213 count_mol
+= 3*plist
[i
].nr
;
1215 else if (interaction_function
[i
].flags
& IF_CONSTRAINT
)
1217 count_mol
+= plist
[i
].nr
;
1221 if (count_mol
> nrdf_internal(&mi
[molb
->type
].atoms
))
1224 "Molecule type '%s' has %d constraints.\n"
1225 "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
1226 *mi
[molb
->type
].name
, count_mol
,
1227 nrdf_internal(&mi
[molb
->type
].atoms
));
1230 count
+= molb
->nmol
*count_mol
;
1236 static void check_gbsa_params_charged(gmx_mtop_t
*sys
, gpp_atomtype_t atype
)
1238 int i
, nmiss
, natoms
, mt
;
1240 const t_atoms
*atoms
;
1243 for (mt
= 0; mt
< sys
->nmoltype
; mt
++)
1245 atoms
= &sys
->moltype
[mt
].atoms
;
1248 for (i
= 0; i
< natoms
; i
++)
1250 q
= atoms
->atom
[i
].q
;
1251 if ((get_atomtype_radius(atoms
->atom
[i
].type
, atype
) == 0 ||
1252 get_atomtype_vol(atoms
->atom
[i
].type
, atype
) == 0 ||
1253 get_atomtype_surftens(atoms
->atom
[i
].type
, atype
) == 0 ||
1254 get_atomtype_gb_radius(atoms
->atom
[i
].type
, atype
) == 0 ||
1255 get_atomtype_S_hct(atoms
->atom
[i
].type
, atype
) == 0) &&
1258 fprintf(stderr
, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
1259 get_atomtype_name(atoms
->atom
[i
].type
, atype
), q
);
1267 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
);
1272 static void check_gbsa_params(gpp_atomtype_t atype
)
1276 /* If we are doing GBSA, check that we got the parameters we need
1277 * This checking is to see if there are GBSA paratmeters for all
1278 * atoms in the force field. To go around this for testing purposes
1279 * comment out the nerror++ counter temporarily
1282 for (i
= 0; i
< get_atomtype_ntypes(atype
); i
++)
1284 if (get_atomtype_radius(i
, atype
) < 0 ||
1285 get_atomtype_vol(i
, atype
) < 0 ||
1286 get_atomtype_surftens(i
, atype
) < 0 ||
1287 get_atomtype_gb_radius(i
, atype
) < 0 ||
1288 get_atomtype_S_hct(i
, atype
) < 0)
1290 fprintf(stderr
, "\nGB parameter(s) missing or negative for atom type '%s'\n",
1291 get_atomtype_name(i
, atype
));
1298 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
);
1303 static real
calc_temp(const gmx_mtop_t
*mtop
,
1304 const t_inputrec
*ir
,
1307 gmx_mtop_atomloop_all_t aloop
;
1312 aloop
= gmx_mtop_atomloop_all_init(mtop
);
1313 while (gmx_mtop_atomloop_all_next(aloop
, &a
, &atom
))
1315 sum_mv2
+= atom
->m
*norm2(v
[a
]);
1319 for (int g
= 0; g
< ir
->opts
.ngtc
; g
++)
1321 nrdf
+= ir
->opts
.nrdf
[g
];
1324 return sum_mv2
/(nrdf
*BOLTZ
);
1327 static real
get_max_reference_temp(const t_inputrec
*ir
,
1336 for (i
= 0; i
< ir
->opts
.ngtc
; i
++)
1338 if (ir
->opts
.tau_t
[i
] < 0)
1344 ref_t
= std::max(ref_t
, ir
->opts
.ref_t
[i
]);
1352 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.",
1360 static void set_verlet_buffer(const gmx_mtop_t
*mtop
,
1366 verletbuf_list_setup_t ls
;
1369 char warn_buf
[STRLEN
];
1371 printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir
->verletbuf_tol
, buffer_temp
);
1373 /* Calculate the buffer size for simple atom vs atoms list */
1374 ls
.cluster_size_i
= 1;
1375 ls
.cluster_size_j
= 1;
1376 calc_verlet_buffer_size(mtop
, det(box
), ir
, buffer_temp
,
1377 &ls
, &n_nonlin_vsite
, &rlist_1x1
);
1379 /* Set the pair-list buffer size in ir */
1380 verletbuf_get_list_setup(FALSE
, FALSE
, &ls
);
1381 calc_verlet_buffer_size(mtop
, det(box
), ir
, buffer_temp
,
1382 &ls
, &n_nonlin_vsite
, &ir
->rlist
);
1384 if (n_nonlin_vsite
> 0)
1386 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
);
1387 warning_note(wi
, warn_buf
);
1390 printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
1391 1, 1, rlist_1x1
, rlist_1x1
-std::max(ir
->rvdw
, ir
->rcoulomb
));
1393 ir
->rlistlong
= ir
->rlist
;
1394 printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
1395 ls
.cluster_size_i
, ls
.cluster_size_j
,
1396 ir
->rlist
, ir
->rlist
-std::max(ir
->rvdw
, ir
->rcoulomb
));
1398 printf("Note that mdrun will redetermine rlist based on the actual pair-list setup\n");
1400 if (sqr(ir
->rlistlong
) >= max_cutoff2(ir
->ePBC
, box
))
1402 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
, std::sqrt(max_cutoff2(ir
->ePBC
, box
)));
1406 int gmx_grompp(int argc
, char *argv
[])
1408 static const char *desc
[] = {
1409 "[THISMODULE] (the gromacs preprocessor)",
1410 "reads a molecular topology file, checks the validity of the",
1411 "file, expands the topology from a molecular description to an atomic",
1412 "description. The topology file contains information about",
1413 "molecule types and the number of molecules, the preprocessor",
1414 "copies each molecule as needed. ",
1415 "There is no limitation on the number of molecule types. ",
1416 "Bonds and bond-angles can be converted into constraints, separately",
1417 "for hydrogens and heavy atoms.",
1418 "Then a coordinate file is read and velocities can be generated",
1419 "from a Maxwellian distribution if requested.",
1420 "[THISMODULE] also reads parameters for [gmx-mdrun] ",
1421 "(eg. number of MD steps, time step, cut-off), and others such as",
1422 "NEMD parameters, which are corrected so that the net acceleration",
1424 "Eventually a binary file is produced that can serve as the sole input",
1425 "file for the MD program.[PAR]",
1427 "[THISMODULE] uses the atom names from the topology file. The atom names",
1428 "in the coordinate file (option [TT]-c[tt]) are only read to generate",
1429 "warnings when they do not match the atom names in the topology.",
1430 "Note that the atom names are irrelevant for the simulation as",
1431 "only the atom types are used for generating interaction parameters.[PAR]",
1433 "[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
1434 "etc. The preprocessor supports the following keywords::",
1437 " #ifndef VARIABLE",
1440 " #define VARIABLE",
1442 " #include \"filename\"",
1443 " #include <filename>",
1445 "The functioning of these statements in your topology may be modulated by",
1446 "using the following two flags in your [REF].mdp[ref] file::",
1448 " define = -DVARIABLE1 -DVARIABLE2",
1449 " include = -I/home/john/doe",
1451 "For further information a C-programming textbook may help you out.",
1452 "Specifying the [TT]-pp[tt] flag will get the pre-processed",
1453 "topology file written out so that you can verify its contents.[PAR]",
1455 "When using position restraints a file with restraint coordinates",
1456 "can be supplied with [TT]-r[tt], otherwise restraining will be done",
1457 "with respect to the conformation from the [TT]-c[tt] option.",
1458 "For free energy calculation the the coordinates for the B topology",
1459 "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
1460 "those of the A topology.[PAR]",
1462 "Starting coordinates can be read from trajectory with [TT]-t[tt].",
1463 "The last frame with coordinates and velocities will be read,",
1464 "unless the [TT]-time[tt] option is used. Only if this information",
1465 "is absent will the coordinates in the [TT]-c[tt] file be used.",
1466 "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
1467 "in your [REF].mdp[ref] file. An energy file can be supplied with",
1468 "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
1471 "[THISMODULE] can be used to restart simulations (preserving",
1472 "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
1473 "However, for simply changing the number of run steps to extend",
1474 "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].",
1475 "You then supply the old checkpoint file directly to [gmx-mdrun]",
1476 "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
1477 "like output frequency, then supplying the checkpoint file to",
1478 "[THISMODULE] with [TT]-t[tt] along with a new [REF].mdp[ref] file",
1479 "with [TT]-f[tt] is the recommended procedure. Actually preserving",
1480 "the ensemble (if possible) still requires passing the checkpoint",
1481 "file to [gmx-mdrun] [TT]-cpi[tt].[PAR]",
1483 "By default, all bonded interactions which have constant energy due to",
1484 "virtual site constructions will be removed. If this constant energy is",
1485 "not zero, this will result in a shift in the total energy. All bonded",
1486 "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
1487 "all constraints for distances which will be constant anyway because",
1488 "of virtual site constructions will be removed. If any constraints remain",
1489 "which involve virtual sites, a fatal error will result.[PAR]"
1491 "To verify your run input file, please take note of all warnings",
1492 "on the screen, and correct where necessary. Do also look at the contents",
1493 "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
1494 "the input that [THISMODULE] has read. If in doubt, you can start [THISMODULE]",
1495 "with the [TT]-debug[tt] option which will give you more information",
1496 "in a file called [TT]grompp.log[tt] (along with real debug info). You",
1497 "can see the contents of the run input file with the [gmx-dump]",
1498 "program. [gmx-check] can be used to compare the contents of two",
1499 "run input files.[PAR]"
1501 "The [TT]-maxwarn[tt] option can be used to override warnings printed",
1502 "by [THISMODULE] that otherwise halt output. In some cases, warnings are",
1503 "harmless, but usually they are not. The user is advised to carefully",
1504 "interpret the output messages before attempting to bypass them with",
1510 t_molinfo
*mi
, *intermolecular_interactions
;
1511 gpp_atomtype_t atype
;
1513 int nvsite
, comb
, mt
;
1519 char fn
[STRLEN
], fnB
[STRLEN
];
1520 const char *mdparin
;
1522 gmx_bool bNeedVel
, bGenVel
;
1523 gmx_bool have_atomnumber
;
1524 gmx_output_env_t
*oenv
;
1525 gmx_bool bVerbose
= FALSE
;
1527 char warn_buf
[STRLEN
];
1530 { efMDP
, NULL
, NULL
, ffREAD
},
1531 { efMDP
, "-po", "mdout", ffWRITE
},
1532 { efSTX
, "-c", NULL
, ffREAD
},
1533 { efSTX
, "-r", NULL
, ffOPTRD
},
1534 { efSTX
, "-rb", NULL
, ffOPTRD
},
1535 { efNDX
, NULL
, NULL
, ffOPTRD
},
1536 { efTOP
, NULL
, NULL
, ffREAD
},
1537 { efTOP
, "-pp", "processed", ffOPTWR
},
1538 { efTPR
, "-o", NULL
, ffWRITE
},
1539 { efTRN
, "-t", NULL
, ffOPTRD
},
1540 { efEDR
, "-e", NULL
, ffOPTRD
},
1541 /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
1542 { efGRO
, "-imd", "imdgroup", ffOPTWR
},
1543 { efTRN
, "-ref", "rotref", ffOPTRW
}
1545 #define NFILE asize(fnm)
1547 /* Command line options */
1548 static gmx_bool bRenum
= TRUE
;
1549 static gmx_bool bRmVSBds
= TRUE
, bZero
= FALSE
;
1550 static int i
, maxwarn
= 0;
1551 static real fr_time
= -1;
1553 { "-v", FALSE
, etBOOL
, {&bVerbose
},
1554 "Be loud and noisy" },
1555 { "-time", FALSE
, etREAL
, {&fr_time
},
1556 "Take frame at or first after this time." },
1557 { "-rmvsbds", FALSE
, etBOOL
, {&bRmVSBds
},
1558 "Remove constant bonded interactions with virtual sites" },
1559 { "-maxwarn", FALSE
, etINT
, {&maxwarn
},
1560 "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
1561 { "-zero", FALSE
, etBOOL
, {&bZero
},
1562 "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
1563 { "-renum", FALSE
, etBOOL
, {&bRenum
},
1564 "Renumber atomtypes and minimize number of atomtypes" }
1567 /* Initiate some variables */
1572 /* Parse the command line */
1573 if (!parse_common_args(&argc
, argv
, 0, NFILE
, fnm
, asize(pa
), pa
,
1574 asize(desc
), desc
, 0, NULL
, &oenv
))
1579 wi
= init_warning(TRUE
, maxwarn
);
1581 /* PARAMETER file processing */
1582 mdparin
= opt2fn("-f", NFILE
, fnm
);
1583 set_warning_line(wi
, mdparin
, -1);
1584 get_ir(mdparin
, opt2fn("-po", NFILE
, fnm
), ir
, opts
, wi
);
1588 fprintf(stderr
, "checking input for internal consistency...\n");
1590 check_ir(mdparin
, ir
, opts
, wi
);
1592 if (ir
->ld_seed
== -1)
1594 ir
->ld_seed
= (gmx_int64_t
)gmx_rng_make_seed();
1595 fprintf(stderr
, "Setting the LD random seed to %" GMX_PRId64
"\n", ir
->ld_seed
);
1598 if (ir
->expandedvals
->lmc_seed
== -1)
1600 ir
->expandedvals
->lmc_seed
= (int)gmx_rng_make_seed();
1601 fprintf(stderr
, "Setting the lambda MC random seed to %d\n", ir
->expandedvals
->lmc_seed
);
1604 bNeedVel
= EI_STATE_VELOCITY(ir
->eI
);
1605 bGenVel
= (bNeedVel
&& opts
->bGenVel
);
1606 if (bGenVel
&& ir
->bContinuation
)
1609 "Generating velocities is inconsistent with attempting "
1610 "to continue a previous run. Choose only one of "
1611 "gen-vel = yes and continuation = yes.");
1612 warning_error(wi
, warn_buf
);
1618 atype
= init_atomtype();
1621 pr_symtab(debug
, 0, "Just opened", &sys
->symtab
);
1624 strcpy(fn
, ftp2fn(efTOP
, NFILE
, fnm
));
1625 if (!gmx_fexist(fn
))
1627 gmx_fatal(FARGS
, "%s does not exist", fn
);
1630 new_status(fn
, opt2fn_null("-pp", NFILE
, fnm
), opt2fn("-c", NFILE
, fnm
),
1631 opts
, ir
, bZero
, bGenVel
, bVerbose
, state
,
1632 atype
, sys
, &nmi
, &mi
, &intermolecular_interactions
,
1633 plist
, &comb
, &reppow
, &fudgeQQ
,
1639 pr_symtab(debug
, 0, "After new_status", &sys
->symtab
);
1643 /* set parameters for virtual site construction (not for vsiten) */
1644 for (mt
= 0; mt
< sys
->nmoltype
; mt
++)
1647 set_vsites(bVerbose
, &sys
->moltype
[mt
].atoms
, atype
, mi
[mt
].plist
);
1649 /* now throw away all obsolete bonds, angles and dihedrals: */
1650 /* note: constraints are ALWAYS removed */
1653 for (mt
= 0; mt
< sys
->nmoltype
; mt
++)
1655 clean_vsite_bondeds(mi
[mt
].plist
, sys
->moltype
[mt
].atoms
.nr
, bRmVSBds
);
1659 if (nvsite
&& ir
->eI
== eiNM
)
1661 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");
1664 if (ir
->cutoff_scheme
== ecutsVERLET
)
1666 fprintf(stderr
, "Removing all charge groups because cutoff-scheme=%s\n",
1667 ecutscheme_names
[ir
->cutoff_scheme
]);
1669 /* Remove all charge groups */
1670 gmx_mtop_remove_chargegroups(sys
);
1673 if (count_constraints(sys
, mi
, wi
) && (ir
->eConstrAlg
== econtSHAKE
))
1675 if (ir
->eI
== eiCG
|| ir
->eI
== eiLBFGS
)
1677 sprintf(warn_buf
, "Can not do %s with %s, use %s",
1678 EI(ir
->eI
), econstr_names
[econtSHAKE
], econstr_names
[econtLINCS
]);
1679 warning_error(wi
, warn_buf
);
1681 if (ir
->bPeriodicMols
)
1683 sprintf(warn_buf
, "Can not do periodic molecules with %s, use %s",
1684 econstr_names
[econtSHAKE
], econstr_names
[econtLINCS
]);
1685 warning_error(wi
, warn_buf
);
1689 if (EI_SD (ir
->eI
) && ir
->etc
!= etcNO
)
1691 warning_note(wi
, "Temperature coupling is ignored with SD integrators.");
1694 /* If we are doing QM/MM, check that we got the atom numbers */
1695 have_atomnumber
= TRUE
;
1696 for (i
= 0; i
< get_atomtype_ntypes(atype
); i
++)
1698 have_atomnumber
= have_atomnumber
&& (get_atomtype_atomnumber(i
, atype
) >= 0);
1700 if (!have_atomnumber
&& ir
->bQMMM
)
1704 "It appears as if you are trying to run a QM/MM calculation, but the force\n"
1705 "field you are using does not contain atom numbers fields. This is an\n"
1706 "optional field (introduced in GROMACS 3.3) for general runs, but mandatory\n"
1707 "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
1708 "an integer just before the mass column in ffXXXnb.itp.\n"
1709 "NB: United atoms have the same atom numbers as normal ones.\n\n");
1714 if ((ir
->adress
->const_wf
> 1) || (ir
->adress
->const_wf
< 0))
1716 warning_error(wi
, "AdResS contant weighting function should be between 0 and 1\n\n");
1718 /** TODO check size of ex+hy width against box size */
1721 /* Check for errors in the input now, since they might cause problems
1722 * during processing further down.
1724 check_warning_error(wi
, FARGS
);
1726 if (opt2bSet("-r", NFILE
, fnm
))
1728 sprintf(fn
, "%s", opt2fn("-r", NFILE
, fnm
));
1732 sprintf(fn
, "%s", opt2fn("-c", NFILE
, fnm
));
1734 if (opt2bSet("-rb", NFILE
, fnm
))
1736 sprintf(fnB
, "%s", opt2fn("-rb", NFILE
, fnm
));
1743 if (nint_ftype(sys
, mi
, F_POSRES
) > 0 || nint_ftype(sys
, mi
, F_FBPOSRES
) > 0)
1747 fprintf(stderr
, "Reading position restraint coords from %s", fn
);
1748 if (strcmp(fn
, fnB
) == 0)
1750 fprintf(stderr
, "\n");
1754 fprintf(stderr
, " and %s\n", fnB
);
1757 gen_posres(sys
, mi
, fn
, fnB
,
1758 ir
->refcoord_scaling
, ir
->ePBC
,
1759 ir
->posres_com
, ir
->posres_comB
,
1763 /* If we are using CMAP, setup the pre-interpolation grid */
1764 if (plist
[F_CMAP
].ncmap
> 0)
1766 init_cmap_grid(&sys
->ffparams
.cmap_grid
, plist
[F_CMAP
].nc
, plist
[F_CMAP
].grid_spacing
);
1767 setup_cmap(plist
[F_CMAP
].grid_spacing
, plist
[F_CMAP
].nc
, plist
[F_CMAP
].cmap
, &sys
->ffparams
.cmap_grid
);
1770 set_wall_atomtype(atype
, opts
, ir
, wi
);
1773 renum_atype(plist
, sys
, ir
->wall_atomtype
, atype
, bVerbose
);
1774 get_atomtype_ntypes(atype
);
1777 if (ir
->implicit_solvent
!= eisNO
)
1779 /* Now we have renumbered the atom types, we can check the GBSA params */
1780 check_gbsa_params(atype
);
1782 /* Check that all atoms that have charge and/or LJ-parameters also have
1783 * sensible GB-parameters
1785 check_gbsa_params_charged(sys
, atype
);
1788 /* PELA: Copy the atomtype data to the topology atomtype list */
1789 copy_atomtype_atomtypes(atype
, &(sys
->atomtypes
));
1793 pr_symtab(debug
, 0, "After renum_atype", &sys
->symtab
);
1798 fprintf(stderr
, "converting bonded parameters...\n");
1801 ntype
= get_atomtype_ntypes(atype
);
1802 convert_params(ntype
, plist
, mi
, intermolecular_interactions
,
1803 comb
, reppow
, fudgeQQ
, sys
);
1807 pr_symtab(debug
, 0, "After convert_params", &sys
->symtab
);
1810 /* set ptype to VSite for virtual sites */
1811 for (mt
= 0; mt
< sys
->nmoltype
; mt
++)
1813 set_vsites_ptype(FALSE
, &sys
->moltype
[mt
]);
1817 pr_symtab(debug
, 0, "After virtual sites", &sys
->symtab
);
1819 /* Check velocity for virtual sites and shells */
1822 check_vel(sys
, state
->v
);
1825 /* check for shells and inpurecs */
1826 check_shells_inputrec(sys
, ir
, wi
);
1831 for (i
= 0; i
< sys
->nmoltype
; i
++)
1833 check_cg_sizes(ftp2fn(efTOP
, NFILE
, fnm
), &sys
->moltype
[i
].cgs
, wi
);
1836 if (EI_DYNAMICS(ir
->eI
) && ir
->eI
!= eiBD
)
1838 check_bonds_timestep(sys
, ir
->delta_t
, wi
);
1841 if (EI_ENERGY_MINIMIZATION(ir
->eI
) && 0 == ir
->nsteps
)
1843 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.");
1846 check_warning_error(wi
, FARGS
);
1850 fprintf(stderr
, "initialising group options...\n");
1852 do_index(mdparin
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1856 if (ir
->cutoff_scheme
== ecutsVERLET
&& ir
->verletbuf_tol
> 0 &&
1859 if (EI_DYNAMICS(ir
->eI
) && inputrec2nboundeddim(ir
) == 3)
1863 if (EI_MD(ir
->eI
) && ir
->etc
== etcNO
)
1867 buffer_temp
= opts
->tempi
;
1871 buffer_temp
= calc_temp(sys
, ir
, state
->v
);
1873 if (buffer_temp
> 0)
1875 sprintf(warn_buf
, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp
);
1876 warning_note(wi
, warn_buf
);
1880 sprintf(warn_buf
, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
1881 (int)(verlet_buffer_ratio_NVE_T0
*100 + 0.5));
1882 warning_note(wi
, warn_buf
);
1887 buffer_temp
= get_max_reference_temp(ir
, wi
);
1890 if (EI_MD(ir
->eI
) && ir
->etc
== etcNO
&& buffer_temp
== 0)
1892 /* NVE with initial T=0: we add a fixed ratio to rlist.
1893 * Since we don't actually use verletbuf_tol, we set it to -1
1894 * so it can't be misused later.
1896 ir
->rlist
*= 1.0 + verlet_buffer_ratio_NVE_T0
;
1897 ir
->verletbuf_tol
= -1;
1901 /* We warn for NVE simulations with a drift tolerance that
1902 * might result in a 1(.1)% drift over the total run-time.
1903 * Note that we can't warn when nsteps=0, since we don't
1904 * know how many steps the user intends to run.
1906 if (EI_MD(ir
->eI
) && ir
->etc
== etcNO
&& ir
->nstlist
> 1 &&
1909 const real driftTolerance
= 0.01;
1910 /* We use 2 DOF per atom = 2kT pot+kin energy,
1911 * to be on the safe side with constraints.
1913 const real totalEnergyDriftPerAtomPerPicosecond
= 2*BOLTZ
*buffer_temp
/(ir
->nsteps
*ir
->delta_t
);
1915 if (ir
->verletbuf_tol
> 1.1*driftTolerance
*totalEnergyDriftPerAtomPerPicosecond
)
1917 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%% when using constraints, you might need to set verlet-buffer-tolerance to %.1e.",
1918 ir
->verletbuf_tol
, ir
->nsteps
*ir
->delta_t
,
1919 (int)(ir
->verletbuf_tol
/totalEnergyDriftPerAtomPerPicosecond
*100 + 0.5),
1920 (int)(100*driftTolerance
+ 0.5),
1921 driftTolerance
*totalEnergyDriftPerAtomPerPicosecond
);
1922 warning_note(wi
, warn_buf
);
1926 set_verlet_buffer(sys
, ir
, buffer_temp
, state
->box
, wi
);
1931 /* Init the temperature coupling state */
1932 init_gtc_state(state
, ir
->opts
.ngtc
, 0, ir
->opts
.nhchainlength
); /* need to add nnhpres here? */
1936 fprintf(stderr
, "Checking consistency between energy and charge groups...\n");
1938 check_eg_vs_cg(sys
);
1942 pr_symtab(debug
, 0, "After index", &sys
->symtab
);
1945 triple_check(mdparin
, ir
, sys
, wi
);
1946 close_symtab(&sys
->symtab
);
1949 pr_symtab(debug
, 0, "After close", &sys
->symtab
);
1952 /* make exclusions between QM atoms */
1955 if (ir
->QMMMscheme
== eQMMMschemenormal
&& ir
->ns_type
== ensSIMPLE
)
1957 gmx_fatal(FARGS
, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
1961 generate_qmexcl(sys
, ir
, wi
);
1965 if (ftp2bSet(efTRN
, NFILE
, fnm
))
1969 fprintf(stderr
, "getting data from old trajectory ...\n");
1971 cont_status(ftp2fn(efTRN
, NFILE
, fnm
), ftp2fn_null(efEDR
, NFILE
, fnm
),
1972 bNeedVel
, bGenVel
, fr_time
, ir
, state
, sys
, oenv
);
1975 if (ir
->ePBC
== epbcXY
&& ir
->nwall
!= 2)
1977 clear_rvec(state
->box
[ZZ
]);
1980 if (ir
->cutoff_scheme
!= ecutsVERLET
&& ir
->rlist
> 0)
1982 set_warning_line(wi
, mdparin
, -1);
1983 check_chargegroup_radii(sys
, ir
, state
->x
, wi
);
1986 if (EEL_FULL(ir
->coulombtype
) || EVDW_PME(ir
->vdwtype
))
1988 /* Calculate the optimal grid dimensions */
1989 copy_mat(state
->box
, box
);
1990 if (ir
->ePBC
== epbcXY
&& ir
->nwall
== 2)
1992 svmul(ir
->wall_ewald_zfac
, box
[ZZ
], box
[ZZ
]);
1994 if (ir
->nkx
> 0 && ir
->nky
> 0 && ir
->nkz
> 0)
1996 /* Mark fourier_spacing as not used */
1997 ir
->fourier_spacing
= 0;
1999 else if (ir
->nkx
!= 0 && ir
->nky
!= 0 && ir
->nkz
!= 0)
2001 set_warning_line(wi
, mdparin
, -1);
2002 warning_error(wi
, "Some of the Fourier grid sizes are set, but all of them need to be set.");
2004 calc_grid(stdout
, box
, ir
->fourier_spacing
,
2005 &(ir
->nkx
), &(ir
->nky
), &(ir
->nkz
));
2008 /* MRS: eventually figure out better logic for initializing the fep
2009 values that makes declaring the lambda and declaring the state not
2010 potentially conflict if not handled correctly. */
2011 if (ir
->efep
!= efepNO
)
2013 state
->fep_state
= ir
->fepvals
->init_fep_state
;
2014 for (i
= 0; i
< efptNR
; i
++)
2016 /* init_lambda trumps state definitions*/
2017 if (ir
->fepvals
->init_lambda
>= 0)
2019 state
->lambda
[i
] = ir
->fepvals
->init_lambda
;
2023 if (ir
->fepvals
->all_lambda
[i
] == NULL
)
2025 gmx_fatal(FARGS
, "Values of lambda not set for a free energy calculation!");
2029 state
->lambda
[i
] = ir
->fepvals
->all_lambda
[i
][state
->fep_state
];
2037 set_pull_init(ir
, sys
, state
->x
, state
->box
, state
->lambda
[efptMASS
], oenv
);
2042 set_reference_positions(ir
->rot
, state
->x
, state
->box
,
2043 opt2fn("-ref", NFILE
, fnm
), opt2bSet("-ref", NFILE
, fnm
),
2047 /* reset_multinr(sys); */
2049 if (EEL_PME(ir
->coulombtype
))
2051 float ratio
= pme_load_estimate(sys
, ir
, state
->box
);
2052 fprintf(stderr
, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio
);
2053 /* With free energy we might need to do PME both for the A and B state
2054 * charges. This will double the cost, but the optimal performance will
2055 * then probably be at a slightly larger cut-off and grid spacing.
2057 if ((ir
->efep
== efepNO
&& ratio
> 1.0/2.0) ||
2058 (ir
->efep
!= efepNO
&& ratio
> 2.0/3.0))
2061 "The optimal PME mesh load for parallel simulations is below 0.5\n"
2062 "and for highly parallel simulations between 0.25 and 0.33,\n"
2063 "for higher performance, increase the cut-off and the PME grid spacing.\n");
2064 if (ir
->efep
!= efepNO
)
2067 "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
2073 char warn_buf
[STRLEN
];
2074 double cio
= compute_io(ir
, sys
->natoms
, &sys
->groups
, F_NRE
, 1);
2075 sprintf(warn_buf
, "This run will generate roughly %.0f Mb of data", cio
);
2078 set_warning_line(wi
, mdparin
, -1);
2079 warning_note(wi
, warn_buf
);
2083 printf("%s\n", warn_buf
);
2089 fprintf(stderr
, "writing run input file...\n");
2092 done_warning(wi
, FARGS
);
2093 write_tpx_state(ftp2fn(efTPR
, NFILE
, fnm
), ir
, state
, sys
);
2095 /* Output IMD group, if bIMD is TRUE */
2096 write_IMDgroup_to_file(ir
->bIMD
, ir
, state
, sys
, NFILE
, fnm
);
2100 done_atomtype(atype
);
2101 done_mtop(sys
, TRUE
);
2102 done_inputrec_strings();