2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
35 /* The make_edi program was generously contributed by Oliver Lange, based
36 * on the code from g_anaeig. You can reach him as olange@gwdg.de. He
37 * probably also holds copyright to the following code.
47 #include "gromacs/legacyheaders/readinp.h"
48 #include "gromacs/commandline/pargs.h"
49 #include "gromacs/legacyheaders/typedefs.h"
50 #include "gromacs/utility/smalloc.h"
51 #include "gromacs/legacyheaders/macros.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/utility/futil.h"
55 #include "gromacs/fileio/pdbio.h"
56 #include "gromacs/fileio/confio.h"
57 #include "gromacs/fileio/tpxio.h"
58 #include "gromacs/fileio/xvgr.h"
59 #include "gromacs/legacyheaders/txtdump.h"
61 #include "gromacs/topology/index.h"
62 #include "gromacs/utility/cstringutil.h"
68 gmx_bool bConstForce; /* Do constant force flooding instead of
69 evaluating a flooding potential */
78 /* This type is for the average, reference, target, and origin structure */
81 int nr; /* number of atoms this structure contains */
82 int *anrs; /* atom index numbers */
83 rvec *x; /* positions */
84 real *sqrtm; /* sqrt of the masses used for mass-
85 * weighting of analysis */
91 int nini; /* total Nr of atoms */
92 gmx_bool fitmas; /* true if trans fit with cm */
93 gmx_bool pcamas; /* true if mass-weighted PCA */
94 int presteps; /* number of steps to run without any
95 * perturbations ... just monitoring */
96 int outfrq; /* freq (in steps) of writing to edo */
97 int maxedsteps; /* max nr of steps per cycle */
98 struct edix sref; /* reference positions, to these fitting
100 struct edix sav; /* average positions */
101 struct edix star; /* target positions */
102 struct edix sori; /* origin positions */
103 real slope; /* minimal slope in acceptance radexp */
104 int ned; /* Nr of atoms in essdyn buffer */
105 t_edflood flood; /* parameters especially for flooding */
110 void make_t_edx(struct edix *edx, int natoms, rvec *pos, atom_id index[])
117 void write_t_edx(FILE *fp, struct edix edx, const char *comment)
119 /*here we copy only the pointers into the t_edx struct
120 no data is copied and edx.box is ignored */
122 fprintf(fp, "#%s \n %d \n", comment, edx.nr);
123 for (i = 0; i < edx.nr; i++)
125 fprintf(fp, "%d %f %f %f\n", (edx.anrs)[i]+1, (edx.x)[i][XX], (edx.x)[i][YY], (edx.x)[i][ZZ]);
129 int sscan_list(int *list[], const char *str, const char *listname)
131 /*this routine scans a string of the form 1,3-6,9 and returns the
132 selected numbers (in this case 1 3 4 5 6 9) in NULL-terminated array of integers.
133 memory for this list will be allocated in this routine -- sscan_list expects *list to
136 listname is a string used in the errormessage*/
141 char *pos, *startpos, *step;
144 /*enums to define the different lexical stati */
146 sBefore, sNumber, sMinus, sRange, sZero, sSmaller, sError, sSteppedRange
149 int status = sBefore; /*status of the deterministic automat to scan str */
153 char *start = NULL; /*holds the string of the number behind a ','*/
154 char *end = NULL; /*holds the string of the number behind a '-' */
156 int nvecs = 0; /* counts the number of vectors in the list*/
168 while ((c = *pos) != 0)
172 /* expect a number */
173 case sBefore: if (isdigit(c))
184 /* have read a number, expect ',' or '-' */
185 case sNumber: if (c == ',')
188 srenew(*list, nvecs+1);
189 (*list)[nvecs++] = number = strtol(start, NULL, 10);
199 status = sMinus; break;
210 /* have read a '-' -> expect a number */
215 status = sRange; break;
227 status = sError; break;
241 /* have read the number after a minus, expect ',' or ':' */
246 end_number = strtol(end, NULL, 10);
247 number = strtol(start, NULL, 10);
251 status = sZero; break;
253 if (end_number <= number)
255 status = sSmaller; break;
257 srenew(*list, nvecs+end_number-number+1);
260 istep = strtol(step, NULL, 10);
267 for (i = number; i <= end_number; i += istep)
269 (*list)[nvecs++] = i;
275 status = sSteppedRange;
287 /* format error occured */
289 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d with char %c", listname, pos-startpos, *(pos-1));
291 /* logical error occured */
293 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid", listname, pos-startpos);
296 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d: second index %d is not bigger than %d", listname, pos-startpos, end_number, number);
299 ++pos; /* read next character */
300 } /*scanner has finished */
302 /* append zero to list of eigenvectors */
303 srenew(*list, nvecs+1);
309 void write_eigvec(FILE* fp, int natoms, int eig_list[], rvec** eigvecs, int nvec, const char *grouptitle, real steps[])
311 /* eig_list is a zero-terminated list of indices into the eigvecs array.
312 eigvecs are coordinates of eigenvectors
313 grouptitle to write in the comment line
314 steps -- array with stepsizes for evLINFIX, evLINACC and evRADACC
317 int n = 0, i; rvec x;
319 while (eig_list[n++])
321 ; /*count selected eigenvecs*/
324 fprintf(fp, "# NUMBER OF EIGENVECTORS + %s\n %d\n", grouptitle, n-1);
326 /* write list of eigenvector indicess */
327 for (n = 0; eig_list[n]; n++)
331 fprintf(fp, "%8d %g\n", eig_list[n], steps[n]);
335 fprintf(fp, "%8d %g\n", eig_list[n], 1.0);
340 /* dump coordinates of the selected eigenvectors */
344 for (i = 0; i < natoms; i++)
346 if (eig_list[n] > nvec)
348 gmx_fatal(FARGS, "Selected eigenvector %d is higher than maximum number %d of available eigenvectors", eig_list[n], nvec);
350 copy_rvec(eigvecs[eig_list[n]-1][i], x);
352 fprintf(fp, "%8.5f %8.5f %8.5f\n", x[XX], x[YY], x[ZZ]);
359 /*enum referring to the different lists of eigenvectors*/
361 evLINFIX, evLINACC, evFLOOD, evRADFIX, evRADACC, evRADCON, evMON, evNr
367 void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
368 int nvec, int *eig_listen[], real* evStepList[])
373 fprintf(fp, "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
374 MAGIC, edpars->nini, edpars->fitmas, edpars->pcamas);
375 fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n",
376 edpars->outfrq, edpars->maxedsteps, edpars->slope);
377 fprintf(fp, "#PRESTEPS\n %d\n#DELTA_F0\n %f\n#INIT_DELTA_F\n %f\n#TAU\n %f\n#EFL_NULL\n %f\n#ALPHA2\n %f\n#KT\n %f\n#HARMONIC\n %d\n#CONST_FORCE_FLOODING\n %d\n",
378 edpars->presteps, edpars->flood.deltaF0, edpars->flood.deltaF, edpars->flood.tau, edpars->flood.constEfl,
379 edpars->flood.alpha2, edpars->flood.kT, edpars->flood.bHarmonic, edpars->flood.bConstForce);
381 /* Average and reference positions */
382 write_t_edx(fp, edpars->sref, "NREF, XREF");
383 write_t_edx(fp, edpars->sav, "NAV, XAV");
387 write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", NULL);
388 write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
389 write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
390 write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
391 write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", NULL);
392 write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", NULL);
393 write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);
396 /*Target and Origin positions */
397 write_t_edx(fp, edpars->star, "NTARGET, XTARGET");
398 write_t_edx(fp, edpars->sori, "NORIGIN, XORIGIN");
401 int read_conffile(const char *confin, char *title, rvec *x[])
403 /* read coordinates out of STX file */
407 printf("read coordnumber from file %s\n", confin);
408 get_stx_coordnum(confin, &natoms);
409 printf("number of coordinates in file %d\n", natoms);
410 /* if (natoms != ncoords)
411 gmx_fatal(FARGS,"number of coordinates in coordinate file (%s, %d)\n"
412 " does not match topology (= %d)",
413 confin,natoms,ncoords);
415 /* make space for coordinates and velocities */
416 init_t_atoms(&confat, natoms, FALSE);
418 read_stx_conf(confin, title, &confat, *x, NULL, NULL, box);
423 void read_eigenvalues(int vecs[], const char *eigfile, real values[],
424 gmx_bool bHesse, real kT)
429 neig = read_xvg(eigfile, &eigval, &nrow);
431 fprintf(stderr, "Read %d eigenvalues\n", neig);
432 for (i = bHesse ? 6 : 0; i < neig; i++)
434 if (eigval[1][i] < -0.001 && bHesse)
437 "WARNING: The Hessian Matrix has negative eigenvalue %f, we set it to zero (no flooding in this direction)\n\n", eigval[1][i]);
440 if (eigval[1][i] < 0)
447 for (i = 0; vecs[i]; i++)
451 gmx_fatal(FARGS, "ERROR: You have chosen one of the first 6 eigenvectors of the HESSE Matrix. That does not make sense, since they correspond to the 6 rotational and translational degrees of freedom.\n\n");
453 values[i] = eigval[1][vecs[i]-1]/kT;
458 for (i = 0; vecs[i]; i++)
460 if (vecs[i] > (neig-6))
462 gmx_fatal(FARGS, "ERROR: You have chosen one of the last 6 eigenvectors of the COVARIANCE Matrix. That does not make sense, since they correspond to the 6 rotational and translational degrees of freedom.\n\n");
464 values[i] = 1/eigval[1][vecs[i]-1];
468 for (i = 0; i < nrow; i++)
476 static real *scan_vecparams(const char *str, const char * par, int nvecs)
478 char f0[256], f1[256]; /*format strings adapted every pass of the loop*/
483 snew(vec_params, nvecs);
487 for (i = 0; (i < nvecs); i++)
489 strcpy(f1, f0); /*f0 is the format string for the "to-be-ignored" numbers*/
490 strcat(f1, "%lf"); /*and f1 to read the actual number in this pass of the loop*/
491 if (sscanf(str, f1, &d) != 1)
493 gmx_fatal(FARGS, "Not enough elements for %s parameter (I need %d)", par, nvecs);
504 void init_edx(struct edix *edx)
511 void filter2edx(struct edix *edx, int nindex, atom_id index[], int ngro,
512 atom_id igro[], rvec *x, const char* structure)
514 /* filter2edx copies coordinates from x to edx which are given in index
520 srenew(edx->x, edx->nr);
521 srenew(edx->anrs, edx->nr);
522 for (i = 0; i < nindex; i++, ix++)
524 for (pos = 0; pos < ngro-1 && igro[pos] != index[i]; ++pos)
527 ; /*search element in igro*/
528 if (igro[pos] != index[i])
530 gmx_fatal(FARGS, "Couldn't find atom with index %d in structure %s", index[i], structure);
532 edx->anrs[ix] = index[i];
533 copy_rvec(x[pos], edx->x[ix]);
537 void get_structure(t_atoms *atoms, const char *IndexFile,
538 const char *StructureFile, struct edix *edx, int nfit,
539 atom_id ifit[], int nav, atom_id index[])
541 atom_id *igro; /*index corresponding to target or origin structure*/
549 ntar = read_conffile(StructureFile, title, &xtar);
550 printf("Select an index group of %d elements that corresponds to the atoms in the structure file %s\n",
551 ntar, StructureFile);
552 get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
555 gmx_fatal(FARGS, "You selected an index group with %d elements instead of %d", ngro, ntar);
558 filter2edx(edx, nfit, ifit, ngro, igro, xtar, StructureFile);
560 /* If average and reference/fitting structure differ, append the average structure as well */
561 if (ifit != index) /*if fit structure is different append these coordinates, too -- don't mind duplicates*/
563 filter2edx(edx, nav, index, ngro, igro, xtar, StructureFile);
567 int gmx_make_edi(int argc, char *argv[])
570 static const char *desc[] = {
571 "[THISMODULE] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
572 "based on eigenvectors of a covariance matrix ([gmx-covar]) or from a",
573 "normal modes analysis ([gmx-nmeig]).",
574 "ED sampling can be used to manipulate the position along collective coordinates",
575 "(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
576 "it may be used to enhance the sampling efficiency of MD simulations by stimulating",
577 "the system to explore new regions along these collective coordinates. A number",
578 "of different algorithms are implemented to drive the system along the eigenvectors",
579 "([TT]-linfix[tt], [TT]-linacc[tt], [TT]-radfix[tt], [TT]-radacc[tt], [TT]-radcon[tt]),",
580 "to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
581 "or to only monitor the projections of the positions onto",
582 "these coordinates ([TT]-mon[tt]).[PAR]",
584 "A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
585 "H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
586 "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[BR]",
587 "B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
588 "Towards an exhaustive sampling of the configurational spaces of the ",
589 "two forms of the peptide hormone guanylin,",
590 "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[BR]",
591 "B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
592 "An extended sampling of the configurational space of HPr from E. coli",
593 "Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
594 "[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
595 "reference structure, target positions, etc.[PAR]",
597 "[TT]-mon[tt]: monitor projections of the coordinates onto selected eigenvectors.[PAR]",
598 "[TT]-linfix[tt]: perform fixed-step linear expansion along selected eigenvectors.[PAR]",
599 "[TT]-linacc[tt]: perform acceptance linear expansion along selected eigenvectors.",
600 "(steps in the desired directions will be accepted, others will be rejected).[PAR]",
601 "[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
602 "[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
603 "(steps in the desired direction will be accepted, others will be rejected).",
604 "[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
605 "expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
606 "to read in a structure file that defines an external origin.[PAR]",
607 "[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
608 "towards a target structure specified with [TT]-tar[tt].[PAR]",
609 "NOTE: each eigenvector can be selected only once. [PAR]",
610 "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].xvg[tt] file[PAR]",
611 "[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
612 "cycle will be started if the spontaneous increase of the radius (in nm/step)",
613 "is less than the value specified.[PAR]",
614 "[TT]-maxedsteps[tt]: maximum number of steps per cycle in radius expansion",
615 "before a new cycle is started.[PAR]",
616 "Note on the parallel implementation: since ED sampling is a 'global' thing",
617 "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
618 "is not very parallel-friendly from an implementation point of view. Because",
619 "parallel ED requires some extra communication, expect the performance to be",
620 "lower as in a free MD simulation, especially on a large number of ranks and/or",
621 "when the ED group contains a lot of atoms. [PAR]",
622 "Please also note that if your ED group contains more than a single protein,",
623 "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
624 "Take a look on the initial RMSD from the reference structure, which is printed",
625 "out at the start of the simulation; if this is much higher than expected, one",
626 "of the ED molecules might be shifted by a box vector. [PAR]",
627 "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].xvg[tt] file",
628 "as a function of time in intervals of OUTFRQ steps.[PAR]",
629 "[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
630 "a single simulation (on different molecules) if several [TT].edi[tt] files were concatenated",
631 "first. The constraints are applied in the order they appear in the [TT].edi[tt] file. ",
632 "Depending on what was specified in the [TT].edi[tt] input file, the output file contains for each ED dataset[PAR]",
633 "[TT]*[tt] the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
634 "[TT]*[tt] projections of the positions onto selected eigenvectors[BR]",
637 "with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
638 "which will lead to extra forces expelling the structure out of the region described",
639 "by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
640 "is kept in that region.",
642 "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
643 "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
644 "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
645 "Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
646 "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
647 "DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
648 "To use constant Efl set [TT]-tau[tt] to zero.",
650 "[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
651 "to give good results for most standard cases in flooding of proteins.",
652 "[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
653 "increase, this is mimicked by [GRK]alpha[grk] > 1.",
654 "For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
656 "RESTART and FLOODING:",
657 "If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
658 "the output file and manually put them into the [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
661 /* Save all the params in this struct and then save it in an edi file.
662 * ignoring fields nmass,massnrs,mass,tmass,nfit,fitnrs,edo
664 static t_edipar edi_params;
667 evStepNr = evRADFIX + 1
669 static const char* evSelections[evNr] = {NULL, NULL, NULL, NULL, NULL, NULL};
670 static const char* evOptions[evNr] = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
671 static const char* evParams[evStepNr] = {NULL, NULL};
672 static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
673 static const char* ConstForceStr;
674 static real * evStepList[evStepNr];
675 static real radstep = 0.0;
676 static real deltaF0 = 150;
677 static real deltaF = 0;
678 static real tau = .1;
679 static real constEfl = 0.0;
680 static real alpha = 1;
681 static int eqSteps = 0;
682 static int * listen[evNr];
683 static real T = 300.0;
684 const real kB = 2.5 / 300.0; /* k_boltzmann in MD units */
685 static gmx_bool bRestrain = FALSE;
686 static gmx_bool bHesse = FALSE;
687 static gmx_bool bHarmonic = FALSE;
689 { "-mon", FALSE, etSTR, {&evSelections[evMON]},
690 "Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91" },
691 { "-linfix", FALSE, etSTR, {&evSelections[0]},
692 "Indices of eigenvectors for fixed increment linear sampling" },
693 { "-linacc", FALSE, etSTR, {&evSelections[1]},
694 "Indices of eigenvectors for acceptance linear sampling" },
695 { "-radfix", FALSE, etSTR, {&evSelections[3]},
696 "Indices of eigenvectors for fixed increment radius expansion" },
697 { "-radacc", FALSE, etSTR, {&evSelections[4]},
698 "Indices of eigenvectors for acceptance radius expansion" },
699 { "-radcon", FALSE, etSTR, {&evSelections[5]},
700 "Indices of eigenvectors for acceptance radius contraction" },
701 { "-flood", FALSE, etSTR, {&evSelections[2]},
702 "Indices of eigenvectors for flooding"},
703 { "-outfrq", FALSE, etINT, {&edi_params.outfrq},
704 "Freqency (in steps) of writing output in [TT].xvg[tt] file" },
705 { "-slope", FALSE, etREAL, { &edi_params.slope},
706 "Minimal slope in acceptance radius expansion"},
707 { "-linstep", FALSE, etSTR, {&evParams[0]},
708 "Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
709 { "-accdir", FALSE, etSTR, {&evParams[1]},
710 "Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
711 { "-radstep", FALSE, etREAL, {&radstep},
712 "Stepsize (nm/step) for fixed increment radius expansion"},
713 { "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
714 "Maximum number of steps per cycle" },
715 { "-eqsteps", FALSE, etINT, {&eqSteps},
716 "Number of steps to run without any perturbations "},
717 { "-deltaF0", FALSE, etREAL, {&deltaF0},
718 "Target destabilization energy for flooding"},
719 { "-deltaF", FALSE, etREAL, {&deltaF},
720 "Start deltaF with this parameter - default 0, nonzero values only needed for restart"},
721 { "-tau", FALSE, etREAL, {&tau},
722 "Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength"},
723 { "-Eflnull", FALSE, etREAL, {&constEfl},
724 "The starting value of the flooding strength. The flooding strength is updated "
725 "according to the adaptive flooding scheme. For a constant flooding strength use [TT]-tau[tt] 0. "},
726 { "-T", FALSE, etREAL, {&T},
727 "T is temperature, the value is needed if you want to do flooding "},
728 { "-alpha", FALSE, etREAL, {&alpha},
729 "Scale width of gaussian flooding potential with alpha^2 "},
730 { "-restrain", FALSE, etBOOL, {&bRestrain},
731 "Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential"},
732 { "-hessian", FALSE, etBOOL, {&bHesse},
733 "The eigenvectors and eigenvalues are from a Hessian matrix"},
734 { "-harmonic", FALSE, etBOOL, {&bHarmonic},
735 "The eigenvalues are interpreted as spring constant"},
736 { "-constF", FALSE, etSTR, {&ConstForceStr},
737 "Constant force flooding: manually set the forces for the eigenvectors selected with -flood "
738 "(put in quotes! \"1.0 2.3 5.1 -3.1\"). No other flooding parameters are needed when specifying the forces directly."}
740 #define NPA asize(pa)
743 int nvec1, *eignr1 = NULL;
744 rvec *xav1, **eigvec1 = NULL;
745 t_atoms *atoms = NULL;
746 int nav; /* Number of atoms in the average structure */
748 const char *indexfile;
750 atom_id *index, *ifit;
751 int nfit; /* Number of atoms in the reference/fit structure */
752 int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
754 real *eigval1 = NULL; /* in V3.3 this is parameter of read_eigenvectors */
757 const char *TargetFile;
758 const char *OriginFile;
759 const char *EigvecFile;
763 /*to read topology file*/
769 gmx_bool bTop, bFit1;
772 { efTRN, "-f", "eigenvec", ffREAD },
773 { efXVG, "-eig", "eigenval", ffOPTRD },
774 { efTPS, NULL, NULL, ffREAD },
775 { efNDX, NULL, NULL, ffOPTRD },
776 { efSTX, "-tar", "target", ffOPTRD},
777 { efSTX, "-ori", "origin", ffOPTRD},
778 { efEDI, "-o", "sam", ffWRITE }
780 #define NFILE asize(fnm)
781 edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
782 if (!parse_common_args(&argc, argv, 0,
783 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
788 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
789 EdiFile = ftp2fn(efEDI, NFILE, fnm);
790 TargetFile = opt2fn_null("-tar", NFILE, fnm);
791 OriginFile = opt2fn_null("-ori", NFILE, fnm);
794 for (ev_class = 0; ev_class < evNr; ++ev_class)
796 if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
798 /*get list of eigenvectors*/
799 nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
800 if (ev_class < evStepNr-2)
802 /*if apropriate get list of stepsizes for these eigenvectors*/
803 if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
805 evStepList[ev_class] =
806 scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
808 else /*if list is not given fill with zeros */
810 snew(evStepList[ev_class], nvecs);
811 for (i = 0; i < nvecs; i++)
813 evStepList[ev_class][i] = 0.0;
817 else if (ev_class == evRADFIX)
819 snew(evStepList[ev_class], nvecs);
820 for (i = 0; i < nvecs; i++)
822 evStepList[ev_class][i] = radstep;
825 else if (ev_class == evFLOOD)
827 snew(evStepList[ev_class], nvecs);
829 /* Are we doing constant force flooding? In that case, we read in
830 * the fproj values from the command line */
831 if (opt2parg_bSet("-constF", NPA, pa))
833 evStepList[ev_class] = scan_vecparams(opt2parg_str("-constF", NPA, pa), "-constF", nvecs);
838 }; /*to avoid ambiguity */
840 else /* if there are no eigenvectors for this option set list to zero */
842 listen[ev_class] = NULL;
843 snew(listen[ev_class], 1);
844 listen[ev_class][0] = 0;
848 /* print the interpreted list of eigenvectors - to give some feedback*/
849 for (ev_class = 0; ev_class < evNr; ++ev_class)
851 printf("Eigenvector list %7s consists of the indices: ", evOptions[ev_class]);
853 while (listen[ev_class][i])
855 printf("%d ", listen[ev_class][i++]);
860 EigvecFile = opt2fn("-f", NFILE, fnm);
862 /*read eigenvectors from eigvec.trr*/
863 read_eigenvectors(EigvecFile, &nav, &bFit1,
864 &xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
866 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
867 title, &top, &ePBC, &xtop, NULL, topbox, 0);
871 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", nav);
872 get_index(atoms, indexfile, 1, &i, &index, &grpname); /*if indexfile != NULL parameter 'atoms' is ignored */
875 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
885 /* if g_covar used different coordinate groups to fit and to do the PCA */
886 printf("\nNote: the structure in %s should be the same\n"
887 " as the one used for the fit in g_covar\n", ftp2fn(efTPS, NFILE, fnm));
888 printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
892 printf("\nNote: Apparently no fitting was done in g_covar.\n"
893 " However, you need to select a reference group for fitting in mdrun\n");
895 get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
897 for (i = 0; i < nfit; i++)
899 copy_rvec(xtop[ifit[i]], xref1[i]);
908 if (opt2parg_bSet("-constF", NPA, pa))
910 /* Constant force flooding is special: Most of the normal flooding
911 * options are not needed. */
912 edi_params.flood.bConstForce = TRUE;
916 /* For normal flooding read eigenvalues and store them in evSteplist[evFLOOD] */
918 if (listen[evFLOOD][0] != 0)
920 read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB*T);
923 edi_params.flood.tau = tau;
924 edi_params.flood.deltaF0 = deltaF0;
925 edi_params.flood.deltaF = deltaF;
926 edi_params.presteps = eqSteps;
927 edi_params.flood.kT = kB*T;
928 edi_params.flood.bHarmonic = bHarmonic;
931 /* Trick: invert sign of Efl and alpha2 then this will give the same sign in the exponential and inverted sign outside */
932 edi_params.flood.constEfl = -constEfl;
933 edi_params.flood.alpha2 = -sqr(alpha);
937 edi_params.flood.constEfl = constEfl;
938 edi_params.flood.alpha2 = sqr(alpha);
942 edi_params.ned = nav;
944 /*number of system atoms */
945 edi_params.nini = atoms->nr;
948 /*store reference and average structure in edi_params*/
949 make_t_edx(&edi_params.sref, nfit, xref1, ifit );
950 make_t_edx(&edi_params.sav, nav, xav1, index);
953 /* Store target positions in edi_params */
954 if (opt2bSet("-tar", NFILE, fnm))
956 if (0 != listen[evFLOOD][0])
958 fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
959 " You may want to use -ori to define the flooding potential center.\n\n");
961 get_structure(atoms, indexfile, TargetFile, &edi_params.star, nfit, ifit, nav, index);
965 make_t_edx(&edi_params.star, 0, NULL, index);
968 /* Store origin positions */
969 if (opt2bSet("-ori", NFILE, fnm))
971 get_structure(atoms, indexfile, OriginFile, &edi_params.sori, nfit, ifit, nav, index);
975 make_t_edx(&edi_params.sori, 0, NULL, index);
979 write_the_whole_thing(gmx_ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);