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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.
46 #include "gromacs/commandline/pargs.h"
48 #include "gromacs/utility/smalloc.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/math/vec.h"
52 #include "gromacs/utility/futil.h"
53 #include "gromacs/fileio/pdbio.h"
54 #include "gromacs/fileio/confio.h"
55 #include "gromacs/fileio/tpxio.h"
56 #include "gromacs/fileio/xvgr.h"
59 #include "gromacs/topology/index.h"
60 #include "gromacs/utility/cstringutil.h"
66 gmx_bool bConstForce; /* Do constant force flooding instead of
67 evaluating a flooding potential */
76 /* This type is for the average, reference, target, and origin structure */
79 int nr; /* number of atoms this structure contains */
80 int *anrs; /* atom index numbers */
81 rvec *x; /* positions */
82 real *sqrtm; /* sqrt of the masses used for mass-
83 * weighting of analysis */
89 int nini; /* total Nr of atoms */
90 gmx_bool fitmas; /* true if trans fit with cm */
91 gmx_bool pcamas; /* true if mass-weighted PCA */
92 int presteps; /* number of steps to run without any
93 * perturbations ... just monitoring */
94 int outfrq; /* freq (in steps) of writing to edo */
95 int maxedsteps; /* max nr of steps per cycle */
96 struct edix sref; /* reference positions, to these fitting
98 struct edix sav; /* average positions */
99 struct edix star; /* target positions */
100 struct edix sori; /* origin positions */
101 real slope; /* minimal slope in acceptance radexp */
102 int ned; /* Nr of atoms in essdyn buffer */
103 t_edflood flood; /* parameters especially for flooding */
108 void make_t_edx(struct edix *edx, int natoms, rvec *pos, atom_id index[])
115 void write_t_edx(FILE *fp, struct edix edx, const char *comment)
117 /*here we copy only the pointers into the t_edx struct
118 no data is copied and edx.box is ignored */
120 fprintf(fp, "#%s \n %d \n", comment, edx.nr);
121 for (i = 0; i < edx.nr; i++)
123 fprintf(fp, "%d %f %f %f\n", (edx.anrs)[i]+1, (edx.x)[i][XX], (edx.x)[i][YY], (edx.x)[i][ZZ]);
127 int sscan_list(int *list[], const char *str, const char *listname)
129 /*this routine scans a string of the form 1,3-6,9 and returns the
130 selected numbers (in this case 1 3 4 5 6 9) in NULL-terminated array of integers.
131 memory for this list will be allocated in this routine -- sscan_list expects *list to
134 listname is a string used in the errormessage*/
139 char *pos, *startpos, *step;
142 /*enums to define the different lexical stati */
144 sBefore, sNumber, sMinus, sRange, sZero, sSmaller, sError, sSteppedRange
147 int status = sBefore; /*status of the deterministic automat to scan str */
151 char *start = NULL; /*holds the string of the number behind a ','*/
152 char *end = NULL; /*holds the string of the number behind a '-' */
154 int nvecs = 0; /* counts the number of vectors in the list*/
166 while ((c = *pos) != 0)
170 /* expect a number */
171 case sBefore: if (isdigit(c))
182 /* have read a number, expect ',' or '-' */
183 case sNumber: if (c == ',')
186 srenew(*list, nvecs+1);
187 (*list)[nvecs++] = number = strtol(start, NULL, 10);
197 status = sMinus; break;
208 /* have read a '-' -> expect a number */
213 status = sRange; break;
225 status = sError; break;
239 /* have read the number after a minus, expect ',' or ':' */
244 end_number = strtol(end, NULL, 10);
245 number = strtol(start, NULL, 10);
249 status = sZero; break;
251 if (end_number <= number)
253 status = sSmaller; break;
255 srenew(*list, nvecs+end_number-number+1);
258 istep = strtol(step, NULL, 10);
265 for (i = number; i <= end_number; i += istep)
267 (*list)[nvecs++] = i;
273 status = sSteppedRange;
285 /* format error occured */
287 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d with char %c", listname, pos-startpos, *(pos-1));
289 /* logical error occured */
291 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid", listname, pos-startpos);
294 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);
297 ++pos; /* read next character */
298 } /*scanner has finished */
300 /* append zero to list of eigenvectors */
301 srenew(*list, nvecs+1);
307 void write_eigvec(FILE* fp, int natoms, int eig_list[], rvec** eigvecs, int nvec, const char *grouptitle, real steps[])
309 /* eig_list is a zero-terminated list of indices into the eigvecs array.
310 eigvecs are coordinates of eigenvectors
311 grouptitle to write in the comment line
312 steps -- array with stepsizes for evLINFIX, evLINACC and evRADACC
315 int n = 0, i; rvec x;
317 while (eig_list[n++])
319 ; /*count selected eigenvecs*/
322 fprintf(fp, "# NUMBER OF EIGENVECTORS + %s\n %d\n", grouptitle, n-1);
324 /* write list of eigenvector indicess */
325 for (n = 0; eig_list[n]; n++)
329 fprintf(fp, "%8d %g\n", eig_list[n], steps[n]);
333 fprintf(fp, "%8d %g\n", eig_list[n], 1.0);
338 /* dump coordinates of the selected eigenvectors */
342 for (i = 0; i < natoms; i++)
344 if (eig_list[n] > nvec)
346 gmx_fatal(FARGS, "Selected eigenvector %d is higher than maximum number %d of available eigenvectors", eig_list[n], nvec);
348 copy_rvec(eigvecs[eig_list[n]-1][i], x);
350 fprintf(fp, "%8.5f %8.5f %8.5f\n", x[XX], x[YY], x[ZZ]);
357 /*enum referring to the different lists of eigenvectors*/
359 evLINFIX, evLINACC, evFLOOD, evRADFIX, evRADACC, evRADCON, evMON, evNr
365 void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
366 int nvec, int *eig_listen[], real* evStepList[])
371 fprintf(fp, "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
372 MAGIC, edpars->nini, edpars->fitmas, edpars->pcamas);
373 fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n",
374 edpars->outfrq, edpars->maxedsteps, edpars->slope);
375 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",
376 edpars->presteps, edpars->flood.deltaF0, edpars->flood.deltaF, edpars->flood.tau, edpars->flood.constEfl,
377 edpars->flood.alpha2, edpars->flood.kT, edpars->flood.bHarmonic, edpars->flood.bConstForce);
379 /* Average and reference positions */
380 write_t_edx(fp, edpars->sref, "NREF, XREF");
381 write_t_edx(fp, edpars->sav, "NAV, XAV");
385 write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", NULL);
386 write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
387 write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
388 write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
389 write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", NULL);
390 write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", NULL);
391 write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);
394 /*Target and Origin positions */
395 write_t_edx(fp, edpars->star, "NTARGET, XTARGET");
396 write_t_edx(fp, edpars->sori, "NORIGIN, XORIGIN");
399 int read_conffile(const char *confin, char *title, rvec *x[])
401 /* read coordinates out of STX file */
405 printf("read coordnumber from file %s\n", confin);
406 get_stx_coordnum(confin, &natoms);
407 printf("number of coordinates in file %d\n", natoms);
408 /* if (natoms != ncoords)
409 gmx_fatal(FARGS,"number of coordinates in coordinate file (%s, %d)\n"
410 " does not match topology (= %d)",
411 confin,natoms,ncoords);
413 /* make space for coordinates and velocities */
414 init_t_atoms(&confat, natoms, FALSE);
416 read_stx_conf(confin, title, &confat, *x, NULL, NULL, box);
421 void read_eigenvalues(int vecs[], const char *eigfile, real values[],
422 gmx_bool bHesse, real kT)
427 neig = read_xvg(eigfile, &eigval, &nrow);
429 fprintf(stderr, "Read %d eigenvalues\n", neig);
430 for (i = bHesse ? 6 : 0; i < neig; i++)
432 if (eigval[1][i] < -0.001 && bHesse)
435 "WARNING: The Hessian Matrix has negative eigenvalue %f, we set it to zero (no flooding in this direction)\n\n", eigval[1][i]);
438 if (eigval[1][i] < 0)
445 for (i = 0; vecs[i]; i++)
449 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");
451 values[i] = eigval[1][vecs[i]-1]/kT;
456 for (i = 0; vecs[i]; i++)
458 if (vecs[i] > (neig-6))
460 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");
462 values[i] = 1/eigval[1][vecs[i]-1];
466 for (i = 0; i < nrow; i++)
474 static real *scan_vecparams(const char *str, const char * par, int nvecs)
476 char f0[256], f1[256]; /*format strings adapted every pass of the loop*/
481 snew(vec_params, nvecs);
485 for (i = 0; (i < nvecs); i++)
487 strcpy(f1, f0); /*f0 is the format string for the "to-be-ignored" numbers*/
488 strcat(f1, "%lf"); /*and f1 to read the actual number in this pass of the loop*/
489 if (sscanf(str, f1, &d) != 1)
491 gmx_fatal(FARGS, "Not enough elements for %s parameter (I need %d)", par, nvecs);
502 void init_edx(struct edix *edx)
509 void filter2edx(struct edix *edx, int nindex, atom_id index[], int ngro,
510 atom_id igro[], rvec *x, const char* structure)
512 /* filter2edx copies coordinates from x to edx which are given in index
518 srenew(edx->x, edx->nr);
519 srenew(edx->anrs, edx->nr);
520 for (i = 0; i < nindex; i++, ix++)
522 for (pos = 0; pos < ngro-1 && igro[pos] != index[i]; ++pos)
525 ; /*search element in igro*/
526 if (igro[pos] != index[i])
528 gmx_fatal(FARGS, "Couldn't find atom with index %d in structure %s", index[i], structure);
530 edx->anrs[ix] = index[i];
531 copy_rvec(x[pos], edx->x[ix]);
535 void get_structure(t_atoms *atoms, const char *IndexFile,
536 const char *StructureFile, struct edix *edx, int nfit,
537 atom_id ifit[], int nav, atom_id index[])
539 atom_id *igro; /*index corresponding to target or origin structure*/
547 ntar = read_conffile(StructureFile, title, &xtar);
548 printf("Select an index group of %d elements that corresponds to the atoms in the structure file %s\n",
549 ntar, StructureFile);
550 get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
553 gmx_fatal(FARGS, "You selected an index group with %d elements instead of %d", ngro, ntar);
556 filter2edx(edx, nfit, ifit, ngro, igro, xtar, StructureFile);
558 /* If average and reference/fitting structure differ, append the average structure as well */
559 if (ifit != index) /*if fit structure is different append these coordinates, too -- don't mind duplicates*/
561 filter2edx(edx, nav, index, ngro, igro, xtar, StructureFile);
565 int gmx_make_edi(int argc, char *argv[])
568 static const char *desc[] = {
569 "[THISMODULE] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
570 "based on eigenvectors of a covariance matrix ([gmx-covar]) or from a",
571 "normal modes analysis ([gmx-nmeig]).",
572 "ED sampling can be used to manipulate the position along collective coordinates",
573 "(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
574 "it may be used to enhance the sampling efficiency of MD simulations by stimulating",
575 "the system to explore new regions along these collective coordinates. A number",
576 "of different algorithms are implemented to drive the system along the eigenvectors",
577 "([TT]-linfix[tt], [TT]-linacc[tt], [TT]-radfix[tt], [TT]-radacc[tt], [TT]-radcon[tt]),",
578 "to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
579 "or to only monitor the projections of the positions onto",
580 "these coordinates ([TT]-mon[tt]).[PAR]",
582 "A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
583 "H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
584 "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[BR]",
585 "B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
586 "Towards an exhaustive sampling of the configurational spaces of the ",
587 "two forms of the peptide hormone guanylin,",
588 "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[BR]",
589 "B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
590 "An extended sampling of the configurational space of HPr from E. coli",
591 "Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
592 "[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
593 "reference structure, target positions, etc.[PAR]",
595 "[TT]-mon[tt]: monitor projections of the coordinates onto selected eigenvectors.[PAR]",
596 "[TT]-linfix[tt]: perform fixed-step linear expansion along selected eigenvectors.[PAR]",
597 "[TT]-linacc[tt]: perform acceptance linear expansion along selected eigenvectors.",
598 "(steps in the desired directions will be accepted, others will be rejected).[PAR]",
599 "[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
600 "[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
601 "(steps in the desired direction will be accepted, others will be rejected).",
602 "[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
603 "expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
604 "to read in a structure file that defines an external origin.[PAR]",
605 "[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
606 "towards a target structure specified with [TT]-tar[tt].[PAR]",
607 "NOTE: each eigenvector can be selected only once. [PAR]",
608 "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].xvg[tt] file[PAR]",
609 "[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
610 "cycle will be started if the spontaneous increase of the radius (in nm/step)",
611 "is less than the value specified.[PAR]",
612 "[TT]-maxedsteps[tt]: maximum number of steps per cycle in radius expansion",
613 "before a new cycle is started.[PAR]",
614 "Note on the parallel implementation: since ED sampling is a 'global' thing",
615 "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
616 "is not very parallel-friendly from an implementation point of view. Because",
617 "parallel ED requires some extra communication, expect the performance to be",
618 "lower as in a free MD simulation, especially on a large number of ranks and/or",
619 "when the ED group contains a lot of atoms. [PAR]",
620 "Please also note that if your ED group contains more than a single protein,",
621 "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
622 "Take a look on the initial RMSD from the reference structure, which is printed",
623 "out at the start of the simulation; if this is much higher than expected, one",
624 "of the ED molecules might be shifted by a box vector. [PAR]",
625 "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].xvg[tt] file",
626 "as a function of time in intervals of OUTFRQ steps.[PAR]",
627 "[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
628 "a single simulation (on different molecules) if several [TT].edi[tt] files were concatenated",
629 "first. The constraints are applied in the order they appear in the [TT].edi[tt] file. ",
630 "Depending on what was specified in the [TT].edi[tt] input file, the output file contains for each ED dataset[PAR]",
631 "[TT]*[tt] the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
632 "[TT]*[tt] projections of the positions onto selected eigenvectors[BR]",
635 "with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
636 "which will lead to extra forces expelling the structure out of the region described",
637 "by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
638 "is kept in that region.",
640 "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
641 "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
642 "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
643 "Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
644 "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
645 "DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
646 "To use constant Efl set [TT]-tau[tt] to zero.",
648 "[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
649 "to give good results for most standard cases in flooding of proteins.",
650 "[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
651 "increase, this is mimicked by [GRK]alpha[grk] > 1.",
652 "For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
654 "RESTART and FLOODING:",
655 "If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
656 "the output file and manually put them into the [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
659 /* Save all the params in this struct and then save it in an edi file.
660 * ignoring fields nmass,massnrs,mass,tmass,nfit,fitnrs,edo
662 static t_edipar edi_params;
665 evStepNr = evRADFIX + 1
667 static const char* evSelections[evNr] = {NULL, NULL, NULL, NULL, NULL, NULL};
668 static const char* evOptions[evNr] = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
669 static const char* evParams[evStepNr] = {NULL, NULL};
670 static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
671 static const char* ConstForceStr;
672 static real * evStepList[evStepNr];
673 static real radstep = 0.0;
674 static real deltaF0 = 150;
675 static real deltaF = 0;
676 static real tau = .1;
677 static real constEfl = 0.0;
678 static real alpha = 1;
679 static int eqSteps = 0;
680 static int * listen[evNr];
681 static real T = 300.0;
682 const real kB = 2.5 / 300.0; /* k_boltzmann in MD units */
683 static gmx_bool bRestrain = FALSE;
684 static gmx_bool bHesse = FALSE;
685 static gmx_bool bHarmonic = FALSE;
687 { "-mon", FALSE, etSTR, {&evSelections[evMON]},
688 "Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91" },
689 { "-linfix", FALSE, etSTR, {&evSelections[0]},
690 "Indices of eigenvectors for fixed increment linear sampling" },
691 { "-linacc", FALSE, etSTR, {&evSelections[1]},
692 "Indices of eigenvectors for acceptance linear sampling" },
693 { "-radfix", FALSE, etSTR, {&evSelections[3]},
694 "Indices of eigenvectors for fixed increment radius expansion" },
695 { "-radacc", FALSE, etSTR, {&evSelections[4]},
696 "Indices of eigenvectors for acceptance radius expansion" },
697 { "-radcon", FALSE, etSTR, {&evSelections[5]},
698 "Indices of eigenvectors for acceptance radius contraction" },
699 { "-flood", FALSE, etSTR, {&evSelections[2]},
700 "Indices of eigenvectors for flooding"},
701 { "-outfrq", FALSE, etINT, {&edi_params.outfrq},
702 "Freqency (in steps) of writing output in [TT].xvg[tt] file" },
703 { "-slope", FALSE, etREAL, { &edi_params.slope},
704 "Minimal slope in acceptance radius expansion"},
705 { "-linstep", FALSE, etSTR, {&evParams[0]},
706 "Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
707 { "-accdir", FALSE, etSTR, {&evParams[1]},
708 "Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
709 { "-radstep", FALSE, etREAL, {&radstep},
710 "Stepsize (nm/step) for fixed increment radius expansion"},
711 { "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
712 "Maximum number of steps per cycle" },
713 { "-eqsteps", FALSE, etINT, {&eqSteps},
714 "Number of steps to run without any perturbations "},
715 { "-deltaF0", FALSE, etREAL, {&deltaF0},
716 "Target destabilization energy for flooding"},
717 { "-deltaF", FALSE, etREAL, {&deltaF},
718 "Start deltaF with this parameter - default 0, nonzero values only needed for restart"},
719 { "-tau", FALSE, etREAL, {&tau},
720 "Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength"},
721 { "-Eflnull", FALSE, etREAL, {&constEfl},
722 "The starting value of the flooding strength. The flooding strength is updated "
723 "according to the adaptive flooding scheme. For a constant flooding strength use [TT]-tau[tt] 0. "},
724 { "-T", FALSE, etREAL, {&T},
725 "T is temperature, the value is needed if you want to do flooding "},
726 { "-alpha", FALSE, etREAL, {&alpha},
727 "Scale width of gaussian flooding potential with alpha^2 "},
728 { "-restrain", FALSE, etBOOL, {&bRestrain},
729 "Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential"},
730 { "-hessian", FALSE, etBOOL, {&bHesse},
731 "The eigenvectors and eigenvalues are from a Hessian matrix"},
732 { "-harmonic", FALSE, etBOOL, {&bHarmonic},
733 "The eigenvalues are interpreted as spring constant"},
734 { "-constF", FALSE, etSTR, {&ConstForceStr},
735 "Constant force flooding: manually set the forces for the eigenvectors selected with -flood "
736 "(put in quotes! \"1.0 2.3 5.1 -3.1\"). No other flooding parameters are needed when specifying the forces directly."}
738 #define NPA asize(pa)
741 int nvec1, *eignr1 = NULL;
742 rvec *xav1, **eigvec1 = NULL;
743 t_atoms *atoms = NULL;
744 int nav; /* Number of atoms in the average structure */
746 const char *indexfile;
748 atom_id *index, *ifit;
749 int nfit; /* Number of atoms in the reference/fit structure */
750 int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
752 real *eigval1 = NULL; /* in V3.3 this is parameter of read_eigenvectors */
755 const char *TargetFile;
756 const char *OriginFile;
757 const char *EigvecFile;
761 /*to read topology file*/
767 gmx_bool bTop, bFit1;
770 { efTRN, "-f", "eigenvec", ffREAD },
771 { efXVG, "-eig", "eigenval", ffOPTRD },
772 { efTPS, NULL, NULL, ffREAD },
773 { efNDX, NULL, NULL, ffOPTRD },
774 { efSTX, "-tar", "target", ffOPTRD},
775 { efSTX, "-ori", "origin", ffOPTRD},
776 { efEDI, "-o", "sam", ffWRITE }
778 #define NFILE asize(fnm)
779 edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
780 if (!parse_common_args(&argc, argv, 0,
781 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
786 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
787 EdiFile = ftp2fn(efEDI, NFILE, fnm);
788 TargetFile = opt2fn_null("-tar", NFILE, fnm);
789 OriginFile = opt2fn_null("-ori", NFILE, fnm);
792 for (ev_class = 0; ev_class < evNr; ++ev_class)
794 if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
796 /*get list of eigenvectors*/
797 nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
798 if (ev_class < evStepNr-2)
800 /*if apropriate get list of stepsizes for these eigenvectors*/
801 if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
803 evStepList[ev_class] =
804 scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
806 else /*if list is not given fill with zeros */
808 snew(evStepList[ev_class], nvecs);
809 for (i = 0; i < nvecs; i++)
811 evStepList[ev_class][i] = 0.0;
815 else if (ev_class == evRADFIX)
817 snew(evStepList[ev_class], nvecs);
818 for (i = 0; i < nvecs; i++)
820 evStepList[ev_class][i] = radstep;
823 else if (ev_class == evFLOOD)
825 snew(evStepList[ev_class], nvecs);
827 /* Are we doing constant force flooding? In that case, we read in
828 * the fproj values from the command line */
829 if (opt2parg_bSet("-constF", NPA, pa))
831 evStepList[ev_class] = scan_vecparams(opt2parg_str("-constF", NPA, pa), "-constF", nvecs);
836 }; /*to avoid ambiguity */
838 else /* if there are no eigenvectors for this option set list to zero */
840 listen[ev_class] = NULL;
841 snew(listen[ev_class], 1);
842 listen[ev_class][0] = 0;
846 /* print the interpreted list of eigenvectors - to give some feedback*/
847 for (ev_class = 0; ev_class < evNr; ++ev_class)
849 printf("Eigenvector list %7s consists of the indices: ", evOptions[ev_class]);
851 while (listen[ev_class][i])
853 printf("%d ", listen[ev_class][i++]);
858 EigvecFile = opt2fn("-f", NFILE, fnm);
860 /*read eigenvectors from eigvec.trr*/
861 read_eigenvectors(EigvecFile, &nav, &bFit1,
862 &xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
864 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
865 title, &top, &ePBC, &xtop, NULL, topbox, 0);
869 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", nav);
870 get_index(atoms, indexfile, 1, &i, &index, &grpname); /*if indexfile != NULL parameter 'atoms' is ignored */
873 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
883 /* if g_covar used different coordinate groups to fit and to do the PCA */
884 printf("\nNote: the structure in %s should be the same\n"
885 " as the one used for the fit in g_covar\n", ftp2fn(efTPS, NFILE, fnm));
886 printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
890 printf("\nNote: Apparently no fitting was done in g_covar.\n"
891 " However, you need to select a reference group for fitting in mdrun\n");
893 get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
895 for (i = 0; i < nfit; i++)
897 copy_rvec(xtop[ifit[i]], xref1[i]);
906 if (opt2parg_bSet("-constF", NPA, pa))
908 /* Constant force flooding is special: Most of the normal flooding
909 * options are not needed. */
910 edi_params.flood.bConstForce = TRUE;
914 /* For normal flooding read eigenvalues and store them in evSteplist[evFLOOD] */
916 if (listen[evFLOOD][0] != 0)
918 read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB*T);
921 edi_params.flood.tau = tau;
922 edi_params.flood.deltaF0 = deltaF0;
923 edi_params.flood.deltaF = deltaF;
924 edi_params.presteps = eqSteps;
925 edi_params.flood.kT = kB*T;
926 edi_params.flood.bHarmonic = bHarmonic;
929 /* Trick: invert sign of Efl and alpha2 then this will give the same sign in the exponential and inverted sign outside */
930 edi_params.flood.constEfl = -constEfl;
931 edi_params.flood.alpha2 = -sqr(alpha);
935 edi_params.flood.constEfl = constEfl;
936 edi_params.flood.alpha2 = sqr(alpha);
940 edi_params.ned = nav;
942 /*number of system atoms */
943 edi_params.nini = atoms->nr;
946 /*store reference and average structure in edi_params*/
947 make_t_edx(&edi_params.sref, nfit, xref1, ifit );
948 make_t_edx(&edi_params.sav, nav, xav1, index);
951 /* Store target positions in edi_params */
952 if (opt2bSet("-tar", NFILE, fnm))
954 if (0 != listen[evFLOOD][0])
956 fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
957 " You may want to use -ori to define the flooding potential center.\n\n");
959 get_structure(atoms, indexfile, TargetFile, &edi_params.star, nfit, ifit, nav, index);
963 make_t_edx(&edi_params.star, 0, NULL, index);
966 /* Store origin positions */
967 if (opt2bSet("-ori", NFILE, fnm))
969 get_structure(atoms, indexfile, OriginFile, &edi_params.sori, nfit, ifit, nav, index);
973 make_t_edx(&edi_params.sori, 0, NULL, index);
977 write_the_whole_thing(gmx_ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);