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.
48 #include "gromacs/commandline/pargs.h"
50 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/math/vec.h"
55 #include "gromacs/utility/futil.h"
56 #include "gromacs/fileio/pdbio.h"
57 #include "gromacs/fileio/confio.h"
58 #include "gromacs/fileio/tpxio.h"
60 #include "gromacs/fileio/xvgr.h"
65 #include "gromacs/utility/cstringutil.h"
71 gmx_bool bConstForce; /* Do constant force flooding instead of
72 evaluating a flooding potential */
81 /* This type is for the average, reference, target, and origin structure */
84 int nr; /* number of atoms this structure contains */
85 int *anrs; /* atom index numbers */
86 rvec *x; /* positions */
87 real *sqrtm; /* sqrt of the masses used for mass-
88 * weighting of analysis */
94 int nini; /* total Nr of atoms */
95 gmx_bool fitmas; /* true if trans fit with cm */
96 gmx_bool pcamas; /* true if mass-weighted PCA */
97 int presteps; /* number of steps to run without any
98 * perturbations ... just monitoring */
99 int outfrq; /* freq (in steps) of writing to edo */
100 int maxedsteps; /* max nr of steps per cycle */
101 struct edix sref; /* reference positions, to these fitting
103 struct edix sav; /* average positions */
104 struct edix star; /* target positions */
105 struct edix sori; /* origin positions */
106 real slope; /* minimal slope in acceptance radexp */
107 int ned; /* Nr of atoms in essdyn buffer */
108 t_edflood flood; /* parameters especially for flooding */
113 void make_t_edx(struct edix *edx, int natoms, rvec *pos, atom_id index[])
120 void write_t_edx(FILE *fp, struct edix edx, const char *comment)
122 /*here we copy only the pointers into the t_edx struct
123 no data is copied and edx.box is ignored */
125 fprintf(fp, "#%s \n %d \n", comment, edx.nr);
126 for (i = 0; i < edx.nr; i++)
128 fprintf(fp, "%d %f %f %f\n", (edx.anrs)[i]+1, (edx.x)[i][XX], (edx.x)[i][YY], (edx.x)[i][ZZ]);
132 int sscan_list(int *list[], const char *str, const char *listname)
134 /*this routine scans a string of the form 1,3-6,9 and returns the
135 selected numbers (in this case 1 3 4 5 6 9) in NULL-terminated array of integers.
136 memory for this list will be allocated in this routine -- sscan_list expects *list to
139 listname is a string used in the errormessage*/
144 char *pos, *startpos, *step;
147 /*enums to define the different lexical stati */
149 sBefore, sNumber, sMinus, sRange, sZero, sSmaller, sError, sSteppedRange
152 int status = sBefore; /*status of the deterministic automat to scan str */
156 char *start = NULL; /*holds the string of the number behind a ','*/
157 char *end = NULL; /*holds the string of the number behind a '-' */
159 int nvecs = 0; /* counts the number of vectors in the list*/
171 while ((c = *pos) != 0)
175 /* expect a number */
176 case sBefore: if (isdigit(c))
187 /* have read a number, expect ',' or '-' */
188 case sNumber: if (c == ',')
191 srenew(*list, nvecs+1);
192 (*list)[nvecs++] = number = strtol(start, NULL, 10);
202 status = sMinus; break;
213 /* have read a '-' -> expect a number */
218 status = sRange; break;
230 status = sError; break;
244 /* have read the number after a minus, expect ',' or ':' */
249 end_number = strtol(end, NULL, 10);
250 number = strtol(start, NULL, 10);
254 status = sZero; break;
256 if (end_number <= number)
258 status = sSmaller; break;
260 srenew(*list, nvecs+end_number-number+1);
263 istep = strtol(step, NULL, 10);
270 for (i = number; i <= end_number; i += istep)
272 (*list)[nvecs++] = i;
278 status = sSteppedRange;
290 /* format error occured */
292 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d with char %c", listname, pos-startpos, *(pos-1));
294 /* logical error occured */
296 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid", listname, pos-startpos);
299 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);
302 ++pos; /* read next character */
303 } /*scanner has finished */
305 /* append zero to list of eigenvectors */
306 srenew(*list, nvecs+1);
312 void write_eigvec(FILE* fp, int natoms, int eig_list[], rvec** eigvecs, int nvec, const char *grouptitle, real steps[])
314 /* eig_list is a zero-terminated list of indices into the eigvecs array.
315 eigvecs are coordinates of eigenvectors
316 grouptitle to write in the comment line
317 steps -- array with stepsizes for evLINFIX, evLINACC and evRADACC
320 int n = 0, i; rvec x;
322 while (eig_list[n++])
324 ; /*count selected eigenvecs*/
327 fprintf(fp, "# NUMBER OF EIGENVECTORS + %s\n %d\n", grouptitle, n-1);
329 /* write list of eigenvector indicess */
330 for (n = 0; eig_list[n]; n++)
334 fprintf(fp, "%8d %g\n", eig_list[n], steps[n]);
338 fprintf(fp, "%8d %g\n", eig_list[n], 1.0);
343 /* dump coordinates of the selected eigenvectors */
347 for (i = 0; i < natoms; i++)
349 if (eig_list[n] > nvec)
351 gmx_fatal(FARGS, "Selected eigenvector %d is higher than maximum number %d of available eigenvectors", eig_list[n], nvec);
353 copy_rvec(eigvecs[eig_list[n]-1][i], x);
355 fprintf(fp, "%8.5f %8.5f %8.5f\n", x[XX], x[YY], x[ZZ]);
362 /*enum referring to the different lists of eigenvectors*/
364 evLINFIX, evLINACC, evFLOOD, evRADFIX, evRADACC, evRADCON, evMON, evNr
370 void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
371 int nvec, int *eig_listen[], real* evStepList[])
376 fprintf(fp, "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
377 MAGIC, edpars->nini, edpars->fitmas, edpars->pcamas);
378 fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n",
379 edpars->outfrq, edpars->maxedsteps, edpars->slope);
380 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",
381 edpars->presteps, edpars->flood.deltaF0, edpars->flood.deltaF, edpars->flood.tau, edpars->flood.constEfl,
382 edpars->flood.alpha2, edpars->flood.kT, edpars->flood.bHarmonic, edpars->flood.bConstForce);
384 /* Average and reference positions */
385 write_t_edx(fp, edpars->sref, "NREF, XREF");
386 write_t_edx(fp, edpars->sav, "NAV, XAV");
390 write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", NULL);
391 write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
392 write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
393 write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
394 write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", NULL);
395 write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", NULL);
396 write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);
399 /*Target and Origin positions */
400 write_t_edx(fp, edpars->star, "NTARGET, XTARGET");
401 write_t_edx(fp, edpars->sori, "NORIGIN, XORIGIN");
404 int read_conffile(const char *confin, char *title, rvec *x[])
406 /* read coordinates out of STX file */
410 printf("read coordnumber from file %s\n", confin);
411 get_stx_coordnum(confin, &natoms);
412 printf("number of coordinates in file %d\n", natoms);
413 /* if (natoms != ncoords)
414 gmx_fatal(FARGS,"number of coordinates in coordinate file (%s, %d)\n"
415 " does not match topology (= %d)",
416 confin,natoms,ncoords);
418 /* make space for coordinates and velocities */
419 init_t_atoms(&confat, natoms, FALSE);
421 read_stx_conf(confin, title, &confat, *x, NULL, NULL, box);
426 void read_eigenvalues(int vecs[], const char *eigfile, real values[],
427 gmx_bool bHesse, real kT)
432 neig = read_xvg(eigfile, &eigval, &nrow);
434 fprintf(stderr, "Read %d eigenvalues\n", neig);
435 for (i = bHesse ? 6 : 0; i < neig; i++)
437 if (eigval[1][i] < -0.001 && bHesse)
440 "WARNING: The Hessian Matrix has negative eigenvalue %f, we set it to zero (no flooding in this direction)\n\n", eigval[1][i]);
443 if (eigval[1][i] < 0)
450 for (i = 0; vecs[i]; i++)
454 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");
456 values[i] = eigval[1][vecs[i]-1]/kT;
461 for (i = 0; vecs[i]; i++)
463 if (vecs[i] > (neig-6))
465 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");
467 values[i] = 1/eigval[1][vecs[i]-1];
471 for (i = 0; i < nrow; i++)
479 static real *scan_vecparams(const char *str, const char * par, int nvecs)
481 char f0[256], f1[256]; /*format strings adapted every pass of the loop*/
486 snew(vec_params, nvecs);
490 for (i = 0; (i < nvecs); i++)
492 strcpy(f1, f0); /*f0 is the format string for the "to-be-ignored" numbers*/
493 strcat(f1, "%lf"); /*and f1 to read the actual number in this pass of the loop*/
494 if (sscanf(str, f1, &d) != 1)
496 gmx_fatal(FARGS, "Not enough elements for %s parameter (I need %d)", par, nvecs);
507 void init_edx(struct edix *edx)
514 void filter2edx(struct edix *edx, int nindex, atom_id index[], int ngro,
515 atom_id igro[], rvec *x, const char* structure)
517 /* filter2edx copies coordinates from x to edx which are given in index
523 srenew(edx->x, edx->nr);
524 srenew(edx->anrs, edx->nr);
525 for (i = 0; i < nindex; i++, ix++)
527 for (pos = 0; pos < ngro-1 && igro[pos] != index[i]; ++pos)
530 ; /*search element in igro*/
531 if (igro[pos] != index[i])
533 gmx_fatal(FARGS, "Couldn't find atom with index %d in structure %s", index[i], structure);
535 edx->anrs[ix] = index[i];
536 copy_rvec(x[pos], edx->x[ix]);
540 void get_structure(t_atoms *atoms, const char *IndexFile,
541 const char *StructureFile, struct edix *edx, int nfit,
542 atom_id ifit[], int nav, atom_id index[])
544 atom_id *igro; /*index corresponding to target or origin structure*/
552 ntar = read_conffile(StructureFile, title, &xtar);
553 printf("Select an index group of %d elements that corresponds to the atoms in the structure file %s\n",
554 ntar, StructureFile);
555 get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
558 gmx_fatal(FARGS, "You selected an index group with %d elements instead of %d", ngro, ntar);
561 filter2edx(edx, nfit, ifit, ngro, igro, xtar, StructureFile);
563 /* If average and reference/fitting structure differ, append the average structure as well */
564 if (ifit != index) /*if fit structure is different append these coordinates, too -- don't mind duplicates*/
566 filter2edx(edx, nav, index, ngro, igro, xtar, StructureFile);
570 int gmx_make_edi(int argc, char *argv[])
573 static const char *desc[] = {
574 "[THISMODULE] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
575 "based on eigenvectors of a covariance matrix ([gmx-covar]) or from a",
576 "normal modes analysis ([gmx-nmeig]).",
577 "ED sampling can be used to manipulate the position along collective coordinates",
578 "(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
579 "it may be used to enhance the sampling efficiency of MD simulations by stimulating",
580 "the system to explore new regions along these collective coordinates. A number",
581 "of different algorithms are implemented to drive the system along the eigenvectors",
582 "([TT]-linfix[tt], [TT]-linacc[tt], [TT]-radfix[tt], [TT]-radacc[tt], [TT]-radcon[tt]),",
583 "to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
584 "or to only monitor the projections of the positions onto",
585 "these coordinates ([TT]-mon[tt]).[PAR]",
587 "A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
588 "H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
589 "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[BR]",
590 "B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
591 "Towards an exhaustive sampling of the configurational spaces of the ",
592 "two forms of the peptide hormone guanylin,",
593 "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[BR]",
594 "B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
595 "An extended sampling of the configurational space of HPr from E. coli",
596 "Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
597 "[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
598 "reference structure, target positions, etc.[PAR]",
600 "[TT]-mon[tt]: monitor projections of the coordinates onto selected eigenvectors.[PAR]",
601 "[TT]-linfix[tt]: perform fixed-step linear expansion along selected eigenvectors.[PAR]",
602 "[TT]-linacc[tt]: perform acceptance linear expansion along selected eigenvectors.",
603 "(steps in the desired directions will be accepted, others will be rejected).[PAR]",
604 "[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
605 "[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
606 "(steps in the desired direction will be accepted, others will be rejected).",
607 "[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
608 "expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
609 "to read in a structure file that defines an external origin.[PAR]",
610 "[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
611 "towards a target structure specified with [TT]-tar[tt].[PAR]",
612 "NOTE: each eigenvector can be selected only once. [PAR]",
613 "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].xvg[tt] file[PAR]",
614 "[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
615 "cycle will be started if the spontaneous increase of the radius (in nm/step)",
616 "is less than the value specified.[PAR]",
617 "[TT]-maxedsteps[tt]: maximum number of steps per cycle in radius expansion",
618 "before a new cycle is started.[PAR]",
619 "Note on the parallel implementation: since ED sampling is a 'global' thing",
620 "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
621 "is not very parallel-friendly from an implementation point of view. Because",
622 "parallel ED requires some extra communication, expect the performance to be",
623 "lower as in a free MD simulation, especially on a large number of nodes and/or",
624 "when the ED group contains a lot of atoms. [PAR]",
625 "Please also note that if your ED group contains more than a single protein,",
626 "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
627 "Take a look on the initial RMSD from the reference structure, which is printed",
628 "out at the start of the simulation; if this is much higher than expected, one",
629 "of the ED molecules might be shifted by a box vector. [PAR]",
630 "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].xvg[tt] file",
631 "as a function of time in intervals of OUTFRQ steps.[PAR]",
632 "[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
633 "a single simulation (on different molecules) if several [TT].edi[tt] files were concatenated",
634 "first. The constraints are applied in the order they appear in the [TT].edi[tt] file. ",
635 "Depending on what was specified in the [TT].edi[tt] input file, the output file contains for each ED dataset[PAR]",
636 "[TT]*[tt] the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
637 "[TT]*[tt] projections of the positions onto selected eigenvectors[BR]",
640 "with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
641 "which will lead to extra forces expelling the structure out of the region described",
642 "by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
643 "is kept in that region.",
645 "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
646 "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
647 "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
648 "Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
649 "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
650 "DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
651 "To use constant Efl set [TT]-tau[tt] to zero.",
653 "[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
654 "to give good results for most standard cases in flooding of proteins.",
655 "[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
656 "increase, this is mimicked by [GRK]alpha[grk] > 1.",
657 "For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
659 "RESTART and FLOODING:",
660 "If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
661 "the output file and manually put them into the [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
664 /* Save all the params in this struct and then save it in an edi file.
665 * ignoring fields nmass,massnrs,mass,tmass,nfit,fitnrs,edo
667 static t_edipar edi_params;
670 evStepNr = evRADFIX + 1
672 static const char* evSelections[evNr] = {NULL, NULL, NULL, NULL, NULL, NULL};
673 static const char* evOptions[evNr] = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
674 static const char* evParams[evStepNr] = {NULL, NULL};
675 static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
676 static const char* ConstForceStr;
677 static real * evStepList[evStepNr];
678 static real radstep = 0.0;
679 static real deltaF0 = 150;
680 static real deltaF = 0;
681 static real tau = .1;
682 static real constEfl = 0.0;
683 static real alpha = 1;
684 static int eqSteps = 0;
685 static int * listen[evNr];
686 static real T = 300.0;
687 const real kB = 2.5 / 300.0; /* k_boltzmann in MD units */
688 static gmx_bool bRestrain = FALSE;
689 static gmx_bool bHesse = FALSE;
690 static gmx_bool bHarmonic = FALSE;
692 { "-mon", FALSE, etSTR, {&evSelections[evMON]},
693 "Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91" },
694 { "-linfix", FALSE, etSTR, {&evSelections[0]},
695 "Indices of eigenvectors for fixed increment linear sampling" },
696 { "-linacc", FALSE, etSTR, {&evSelections[1]},
697 "Indices of eigenvectors for acceptance linear sampling" },
698 { "-radfix", FALSE, etSTR, {&evSelections[3]},
699 "Indices of eigenvectors for fixed increment radius expansion" },
700 { "-radacc", FALSE, etSTR, {&evSelections[4]},
701 "Indices of eigenvectors for acceptance radius expansion" },
702 { "-radcon", FALSE, etSTR, {&evSelections[5]},
703 "Indices of eigenvectors for acceptance radius contraction" },
704 { "-flood", FALSE, etSTR, {&evSelections[2]},
705 "Indices of eigenvectors for flooding"},
706 { "-outfrq", FALSE, etINT, {&edi_params.outfrq},
707 "Freqency (in steps) of writing output in [TT].xvg[tt] file" },
708 { "-slope", FALSE, etREAL, { &edi_params.slope},
709 "Minimal slope in acceptance radius expansion"},
710 { "-linstep", FALSE, etSTR, {&evParams[0]},
711 "Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
712 { "-accdir", FALSE, etSTR, {&evParams[1]},
713 "Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
714 { "-radstep", FALSE, etREAL, {&radstep},
715 "Stepsize (nm/step) for fixed increment radius expansion"},
716 { "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
717 "Maximum number of steps per cycle" },
718 { "-eqsteps", FALSE, etINT, {&eqSteps},
719 "Number of steps to run without any perturbations "},
720 { "-deltaF0", FALSE, etREAL, {&deltaF0},
721 "Target destabilization energy for flooding"},
722 { "-deltaF", FALSE, etREAL, {&deltaF},
723 "Start deltaF with this parameter - default 0, nonzero values only needed for restart"},
724 { "-tau", FALSE, etREAL, {&tau},
725 "Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength"},
726 { "-Eflnull", FALSE, etREAL, {&constEfl},
727 "The starting value of the flooding strength. The flooding strength is updated "
728 "according to the adaptive flooding scheme. For a constant flooding strength use [TT]-tau[tt] 0. "},
729 { "-T", FALSE, etREAL, {&T},
730 "T is temperature, the value is needed if you want to do flooding "},
731 { "-alpha", FALSE, etREAL, {&alpha},
732 "Scale width of gaussian flooding potential with alpha^2 "},
733 { "-restrain", FALSE, etBOOL, {&bRestrain},
734 "Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential"},
735 { "-hessian", FALSE, etBOOL, {&bHesse},
736 "The eigenvectors and eigenvalues are from a Hessian matrix"},
737 { "-harmonic", FALSE, etBOOL, {&bHarmonic},
738 "The eigenvalues are interpreted as spring constant"},
739 { "-constF", FALSE, etSTR, {&ConstForceStr},
740 "Constant force flooding: manually set the forces for the eigenvectors selected with -flood "
741 "(put in quotes! \"1.0 2.3 5.1 -3.1\"). No other flooding parameters are needed when specifying the forces directly."}
743 #define NPA asize(pa)
746 int nvec1, *eignr1 = NULL;
747 rvec *xav1, **eigvec1 = NULL;
748 t_atoms *atoms = NULL;
749 int nav; /* Number of atoms in the average structure */
751 const char *indexfile;
753 atom_id *index, *ifit;
754 int nfit; /* Number of atoms in the reference/fit structure */
755 int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
757 real *eigval1 = NULL; /* in V3.3 this is parameter of read_eigenvectors */
760 const char *TargetFile;
761 const char *OriginFile;
762 const char *EigvecFile;
766 /*to read topology file*/
772 gmx_bool bTop, bFit1;
775 { efTRN, "-f", "eigenvec", ffREAD },
776 { efXVG, "-eig", "eigenval", ffOPTRD },
777 { efTPS, NULL, NULL, ffREAD },
778 { efNDX, NULL, NULL, ffOPTRD },
779 { efSTX, "-tar", "target", ffOPTRD},
780 { efSTX, "-ori", "origin", ffOPTRD},
781 { efEDI, "-o", "sam", ffWRITE }
783 #define NFILE asize(fnm)
784 edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
785 if (!parse_common_args(&argc, argv, 0,
786 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
791 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
792 EdiFile = ftp2fn(efEDI, NFILE, fnm);
793 TargetFile = opt2fn_null("-tar", NFILE, fnm);
794 OriginFile = opt2fn_null("-ori", NFILE, fnm);
797 for (ev_class = 0; ev_class < evNr; ++ev_class)
799 if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
801 /*get list of eigenvectors*/
802 nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
803 if (ev_class < evStepNr-2)
805 /*if apropriate get list of stepsizes for these eigenvectors*/
806 if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
808 evStepList[ev_class] =
809 scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
811 else /*if list is not given fill with zeros */
813 snew(evStepList[ev_class], nvecs);
814 for (i = 0; i < nvecs; i++)
816 evStepList[ev_class][i] = 0.0;
820 else if (ev_class == evRADFIX)
822 snew(evStepList[ev_class], nvecs);
823 for (i = 0; i < nvecs; i++)
825 evStepList[ev_class][i] = radstep;
828 else if (ev_class == evFLOOD)
830 snew(evStepList[ev_class], nvecs);
832 /* Are we doing constant force flooding? In that case, we read in
833 * the fproj values from the command line */
834 if (opt2parg_bSet("-constF", NPA, pa))
836 evStepList[ev_class] = scan_vecparams(opt2parg_str("-constF", NPA, pa), "-constF", nvecs);
841 }; /*to avoid ambiguity */
843 else /* if there are no eigenvectors for this option set list to zero */
845 listen[ev_class] = NULL;
846 snew(listen[ev_class], 1);
847 listen[ev_class][0] = 0;
851 /* print the interpreted list of eigenvectors - to give some feedback*/
852 for (ev_class = 0; ev_class < evNr; ++ev_class)
854 printf("Eigenvector list %7s consists of the indices: ", evOptions[ev_class]);
856 while (listen[ev_class][i])
858 printf("%d ", listen[ev_class][i++]);
863 EigvecFile = opt2fn("-f", NFILE, fnm);
865 /*read eigenvectors from eigvec.trr*/
866 read_eigenvectors(EigvecFile, &nav, &bFit1,
867 &xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
869 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
870 title, &top, &ePBC, &xtop, NULL, topbox, 0);
874 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", nav);
875 get_index(atoms, indexfile, 1, &i, &index, &grpname); /*if indexfile != NULL parameter 'atoms' is ignored */
878 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
888 /* if g_covar used different coordinate groups to fit and to do the PCA */
889 printf("\nNote: the structure in %s should be the same\n"
890 " as the one used for the fit in g_covar\n", ftp2fn(efTPS, NFILE, fnm));
891 printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
895 printf("\nNote: Apparently no fitting was done in g_covar.\n"
896 " However, you need to select a reference group for fitting in mdrun\n");
898 get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
900 for (i = 0; i < nfit; i++)
902 copy_rvec(xtop[ifit[i]], xref1[i]);
911 if (opt2parg_bSet("-constF", NPA, pa))
913 /* Constant force flooding is special: Most of the normal flooding
914 * options are not needed. */
915 edi_params.flood.bConstForce = TRUE;
919 /* For normal flooding read eigenvalues and store them in evSteplist[evFLOOD] */
921 if (listen[evFLOOD][0] != 0)
923 read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB*T);
926 edi_params.flood.tau = tau;
927 edi_params.flood.deltaF0 = deltaF0;
928 edi_params.flood.deltaF = deltaF;
929 edi_params.presteps = eqSteps;
930 edi_params.flood.kT = kB*T;
931 edi_params.flood.bHarmonic = bHarmonic;
934 /* Trick: invert sign of Efl and alpha2 then this will give the same sign in the exponential and inverted sign outside */
935 edi_params.flood.constEfl = -constEfl;
936 edi_params.flood.alpha2 = -sqr(alpha);
940 edi_params.flood.constEfl = constEfl;
941 edi_params.flood.alpha2 = sqr(alpha);
945 edi_params.ned = nav;
947 /*number of system atoms */
948 edi_params.nini = atoms->nr;
951 /*store reference and average structure in edi_params*/
952 make_t_edx(&edi_params.sref, nfit, xref1, ifit );
953 make_t_edx(&edi_params.sav, nav, xav1, index);
956 /* Store target positions in edi_params */
957 if (opt2bSet("-tar", NFILE, fnm))
959 if (0 != listen[evFLOOD][0])
961 fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
962 " You may want to use -ori to define the flooding potential center.\n\n");
964 get_structure(atoms, indexfile, TargetFile, &edi_params.star, nfit, ifit, nav, index);
968 make_t_edx(&edi_params.star, 0, NULL, index);
971 /* Store origin positions */
972 if (opt2bSet("-ori", NFILE, fnm))
974 get_structure(atoms, indexfile, OriginFile, &edi_params.sori, nfit, ifit, nav, index);
978 make_t_edx(&edi_params.sori, 0, NULL, index);
982 write_the_whole_thing(gmx_ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);