src/gromacs/gmxana/gmx_rotmat.cpp

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  35 #include "gmxpre.h"
  36
  37 #include <cmath>
  38 #include <cstring>
  39
  40 #include "gromacs/commandline/pargs.h"
  41 #include "gromacs/commandline/viewit.h"
  42 #include "gromacs/fileio/confio.h"
  43 #include "gromacs/fileio/trxio.h"
  44 #include "gromacs/fileio/xvgr.h"
  45 #include "gromacs/gmxana/gmx_ana.h"
  46 #include "gromacs/math/do_fit.h"
  47 #include "gromacs/math/functions.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/pbcutil/rmpbc.h"
  50 #include "gromacs/topology/index.h"
  51 #include "gromacs/topology/topology.h"
  52 #include "gromacs/utility/arraysize.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "gromacs/utility/gmxassert.h"
  56 #include "gromacs/utility/smalloc.h"
  57
  58 static void get_refx(gmx_output_env_t *oenv, const char *trxfn, int nfitdim, int skip,
  59                      int gnx, int *index,
  60                      gmx_bool bMW, const t_topology *top, int ePBC, rvec *x_ref)
  61 {
  62     int          natoms, nfr_all, nfr, i, j, a, r, c, min_fr;
  63     t_trxstatus *status;
  64     real        *ti, min_t;
  65     double       tot_mass, msd, *srmsd, min_srmsd, srmsd_tot;
  66     rvec        *x, **xi;
  67     real         xf;
  68     matrix       box, R;
  69     real        *w_rls;
  70     gmx_rmpbc_t  gpbc = nullptr;
  71
  72
  73     nfr_all = 0;
  74     nfr     = 0;
  75     snew(ti, 100);
  76     snew(xi, 100);
  77     natoms = read_first_x(oenv, &status, trxfn, &ti[nfr], &x, box);
  78
  79     snew(w_rls, gnx);
  80     tot_mass = 0;
  81     for (a = 0; a < gnx; a++)
  82     {
  83         if (index[a] >= natoms)
  84         {
  85             gmx_fatal(FARGS, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[a]+1, natoms);
  86         }
  87         w_rls[a]  = (bMW ? top->atoms.atom[index[a]].m : 1.0);
  88         tot_mass += w_rls[a];
  89     }
  90     gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
  91
  92     do
  93     {
  94         if (nfr_all % skip == 0)
  95         {
  96             gmx_rmpbc(gpbc, natoms, box, x);
  97             snew(xi[nfr], gnx);
  98             for (i = 0; i < gnx; i++)
  99             {
 100                 copy_rvec(x[index[i]], xi[nfr][i]);
 101             }
 102             reset_x(gnx, nullptr, gnx, nullptr, xi[nfr], w_rls);
 103             nfr++;
 104             if (nfr % 100 == 0)
 105             {
 106                 srenew(ti, nfr+100);
 107                 srenew(xi, nfr+100);
 108             }
 109         }
 110         nfr_all++;
 111     }
 112     while (read_next_x(oenv, status, &ti[nfr], x, box));
 113     close_trx(status);
 114     sfree(x);
 115
 116     gmx_rmpbc_done(gpbc);
 117
 118     snew(srmsd, nfr);
 119     for (i = 0; i < nfr; i++)
 120     {
 121         fprintf(stdout, "\rProcessing frame %d of %d", i, nfr);
 122         fflush(stdout);
 123         for (j = i+1; j < nfr; j++)
 124         {
 125             calc_fit_R(nfitdim, gnx, w_rls, xi[i], xi[j], R);
 126
 127             msd = 0;
 128             for (a = 0; a < gnx; a++)
 129             {
 130                 for (r = 0; r < DIM; r++)
 131                 {
 132                     xf = 0;
 133                     for (c = 0; c < DIM; c++)
 134                     {
 135                         xf += R[r][c]*xi[j][a][c];
 136                     }
 137                     msd += w_rls[a]*gmx::square(xi[i][a][r] - xf);
 138                 }
 139             }
 140             msd      /= tot_mass;
 141             srmsd[i] += std::sqrt(msd);
 142             srmsd[j] += std::sqrt(msd);
 143         }
 144         sfree(xi[i]);
 145     }
 146     printf("\n");
 147     sfree(w_rls);
 148
 149     min_srmsd = GMX_REAL_MAX;
 150     min_fr    = -1;
 151     min_t     = -1;
 152     srmsd_tot = 0;
 153     for (i = 0; i < nfr; i++)
 154     {
 155         srmsd[i] /= (nfr - 1);
 156         if (srmsd[i] < min_srmsd)
 157         {
 158             min_srmsd = srmsd[i];
 159             min_fr    = i;
 160             min_t     = ti[i];
 161         }
 162         srmsd_tot += srmsd[i];
 163     }
 164     sfree(srmsd);
 165
 166     printf("Average RMSD between all structures: %.3f\n", srmsd_tot/nfr);
 167     printf("Structure with lowest RMSD to all others: time %g, av. RMSD %.3f\n",
 168            min_t, min_srmsd);
 169
 170     for (a = 0; a < gnx; a++)
 171     {
 172         copy_rvec(xi[min_fr][a], x_ref[index[a]]);
 173     }
 174
 175     sfree(xi);
 176 }
 177
 178 int gmx_rotmat(int argc, char *argv[])
 179 {
 180     const char       *desc[] = {
 181         "[THISMODULE] plots the rotation matrix required for least squares fitting",
 182         "a conformation onto the reference conformation provided with",
 183         "[TT]-s[tt]. Translation is removed before fitting.",
 184         "The output are the three vectors that give the new directions",
 185         "of the x, y and z directions of the reference conformation,",
 186         "for example: (zx,zy,zz) is the orientation of the reference",
 187         "z-axis in the trajectory frame.",
 188         "[PAR]",
 189         "This tool is useful for, for instance,",
 190         "determining the orientation of a molecule",
 191         "at an interface, possibly on a trajectory produced with",
 192         "[TT]gmx trjconv -fit rotxy+transxy[tt] to remove the rotation",
 193         "in the [IT]x-y[it] plane.",
 194         "[PAR]",
 195         "Option [TT]-ref[tt] determines a reference structure for fitting,",
 196         "instead of using the structure from [TT]-s[tt]. The structure with",
 197         "the lowest sum of RMSD's to all other structures is used.",
 198         "Since the computational cost of this procedure grows with",
 199         "the square of the number of frames, the [TT]-skip[tt] option",
 200         "can be useful. A full fit or only a fit in the [IT]x-y[it] plane can",
 201         "be performed.",
 202         "[PAR]",
 203         "Option [TT]-fitxy[tt] fits in the [IT]x-y[it] plane before determining",
 204         "the rotation matrix."
 205     };
 206     const char       *reffit[] =
 207     { nullptr, "none", "xyz", "xy", nullptr };
 208     static int        skip   = 1;
 209     static gmx_bool   bFitXY = FALSE, bMW = TRUE;
 210     t_pargs           pa[]   = {
 211         { "-ref", FALSE, etENUM, {reffit},
 212           "Determine the optimal reference structure" },
 213         { "-skip", FALSE, etINT, {&skip},
 214           "Use every nr-th frame for [TT]-ref[tt]" },
 215         { "-fitxy", FALSE, etBOOL, {&bFitXY},
 216           "Fit the x/y rotation before determining the rotation" },
 217         { "-mw", FALSE, etBOOL, {&bMW},
 218           "Use mass weighted fitting" }
 219     };
 220     FILE             *out;
 221     t_trxstatus      *status;
 222     t_topology        top;
 223     int               ePBC;
 224     rvec             *x_ref, *x;
 225     matrix            box, R;
 226     real              t;
 227     int               natoms, i;
 228     char             *grpname;
 229     int               gnx;
 230     gmx_rmpbc_t       gpbc = nullptr;
 231     int              *index;
 232     gmx_output_env_t *oenv;
 233     real             *w_rls;
 234     const char       *leg[]  = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
 235 #define NLEG asize(leg)
 236     t_filenm          fnm[] = {
 237         { efTRX, "-f",   nullptr,       ffREAD },
 238         { efTPS, nullptr,   nullptr,       ffREAD },
 239         { efNDX, nullptr,   nullptr,       ffOPTRD },
 240         { efXVG, nullptr,   "rotmat",   ffWRITE }
 241     };
 242 #define NFILE asize(fnm)
 243
 244     if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
 245                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
 246     {
 247         return 0;
 248     }
 249
 250     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x_ref, nullptr, box, bMW);
 251
 252     gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
 253
 254     gmx_rmpbc(gpbc, top.atoms.nr, box, x_ref);
 255
 256     get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 257
 258     GMX_RELEASE_ASSERT(reffit[0] != nullptr, "Options inconsistency; reffit[0] is NULL");
 259     if (reffit[0][0] != 'n')
 260     {
 261         get_refx(oenv, ftp2fn(efTRX, NFILE, fnm), reffit[0][2] == 'z' ? 3 : 2, skip,
 262                  gnx, index, bMW, &top, ePBC, x_ref);
 263     }
 264
 265     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 266
 267     snew(w_rls, natoms);
 268     for (i = 0; i < gnx; i++)
 269     {
 270         if (index[i] >= natoms)
 271         {
 272             gmx_fatal(FARGS, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[i]+1, natoms);
 273         }
 274         w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
 275     }
 276
 277     if (reffit[0][0] == 'n')
 278     {
 279         reset_x(gnx, index, natoms, nullptr, x_ref, w_rls);
 280     }
 281
 282     out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
 283                    "Fit matrix", "Time (ps)", "", oenv);
 284     xvgr_legend(out, NLEG, leg, oenv);
 285
 286     do
 287     {
 288         gmx_rmpbc(gpbc, natoms, box, x);
 289
 290         reset_x(gnx, index, natoms, nullptr, x, w_rls);
 291
 292         if (bFitXY)
 293         {
 294             do_fit_ndim(2, natoms, w_rls, x_ref, x);
 295         }
 296
 297         calc_fit_R(DIM, natoms, w_rls, x_ref, x, R);
 298
 299         fprintf(out,
 300                 "%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
 301                 t,
 302                 R[XX][XX], R[XX][YY], R[XX][ZZ],
 303                 R[YY][XX], R[YY][YY], R[YY][ZZ],
 304                 R[ZZ][XX], R[ZZ][YY], R[ZZ][ZZ]);
 305     }
 306     while (read_next_x(oenv, status, &t, x, box));
 307
 308     gmx_rmpbc_done(gpbc);
 309
 310     close_trx(status);
 311
 312     xvgrclose(out);
 313
 314     do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
 315
 316     return 0;
 317 }