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42 #include "gromacs/commandline/pargs.h"
44 #include "gromacs/utility/smalloc.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/utility/futil.h"
48 #include "gromacs/topology/index.h"
49 #include "gromacs/fileio/xvgr.h"
51 #include "gromacs/pbcutil/rmpbc.h"
52 #include "gromacs/fileio/tpxio.h"
53 #include "gromacs/fileio/trxio.h"
56 #include "gromacs/math/do_fit.h"
58 static void get_refx(output_env_t oenv, const char *trxfn, int nfitdim, int skip,
60 gmx_bool bMW, t_topology *top, int ePBC, rvec *x_ref)
62 int natoms, nfr_all, nfr, i, j, a, r, c, min_fr;
65 double tot_mass, msd, *srmsd, min_srmsd, srmsd_tot;
70 gmx_rmpbc_t gpbc = NULL;
77 natoms = read_first_x(oenv, &status, trxfn, &ti[nfr], &x, box);
81 for (a = 0; a < gnx; a++)
83 if (index[a] >= natoms)
85 gmx_fatal(FARGS, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[a]+1, natoms);
87 w_rls[a] = (bMW ? top->atoms.atom[index[a]].m : 1.0);
90 gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
94 if (nfr_all % skip == 0)
96 gmx_rmpbc(gpbc, natoms, box, x);
98 for (i = 0; i < gnx; i++)
100 copy_rvec(x[index[i]], xi[nfr][i]);
102 reset_x(gnx, NULL, gnx, NULL, xi[nfr], w_rls);
112 while (read_next_x(oenv, status, &ti[nfr], x, box));
116 gmx_rmpbc_done(gpbc);
119 for (i = 0; i < nfr; i++)
121 printf("\rProcessing frame %d of %d", i, nfr);
122 for (j = i+1; j < nfr; j++)
124 calc_fit_R(nfitdim, gnx, w_rls, xi[i], xi[j], R);
127 for (a = 0; a < gnx; a++)
129 for (r = 0; r < DIM; r++)
132 for (c = 0; c < DIM; c++)
134 xf += R[r][c]*xi[j][a][c];
136 msd += w_rls[a]*sqr(xi[i][a][r] - xf);
140 srmsd[i] += sqrt(msd);
141 srmsd[j] += sqrt(msd);
148 min_srmsd = GMX_REAL_MAX;
152 for (i = 0; i < nfr; i++)
154 srmsd[i] /= (nfr - 1);
155 if (srmsd[i] < min_srmsd)
157 min_srmsd = srmsd[i];
161 srmsd_tot += srmsd[i];
165 printf("Average RMSD between all structures: %.3f\n", srmsd_tot/nfr);
166 printf("Structure with lowest RMSD to all others: time %g, av. RMSD %.3f\n",
169 for (a = 0; a < gnx; a++)
171 copy_rvec(xi[min_fr][a], x_ref[index[a]]);
177 int gmx_rotmat(int argc, char *argv[])
179 const char *desc[] = {
180 "[THISMODULE] plots the rotation matrix required for least squares fitting",
181 "a conformation onto the reference conformation provided with",
182 "[TT]-s[tt]. Translation is removed before fitting.",
183 "The output are the three vectors that give the new directions",
184 "of the x, y and z directions of the reference conformation,",
185 "for example: (zx,zy,zz) is the orientation of the reference",
186 "z-axis in the trajectory frame.",
188 "This tool is useful for, for instance,",
189 "determining the orientation of a molecule",
190 "at an interface, possibly on a trajectory produced with",
191 "[TT]gmx trjconv -fit rotxy+transxy[tt] to remove the rotation",
192 "in the [IT]x-y[it] plane.",
194 "Option [TT]-ref[tt] determines a reference structure for fitting,",
195 "instead of using the structure from [TT]-s[tt]. The structure with",
196 "the lowest sum of RMSD's to all other structures is used.",
197 "Since the computational cost of this procedure grows with",
198 "the square of the number of frames, the [TT]-skip[tt] option",
199 "can be useful. A full fit or only a fit in the [IT]x-y[it] plane can",
202 "Option [TT]-fitxy[tt] fits in the [IT]x-y[it] plane before determining",
203 "the rotation matrix."
205 const char *reffit[] =
206 { NULL, "none", "xyz", "xy", NULL };
208 static gmx_bool bFitXY = FALSE, bMW = TRUE;
210 { "-ref", FALSE, etENUM, {reffit},
211 "Determine the optimal reference structure" },
212 { "-skip", FALSE, etINT, {&skip},
213 "Use every nr-th frame for [TT]-ref[tt]" },
214 { "-fitxy", FALSE, etBOOL, {&bFitXY},
215 "Fit the x/y rotation before determining the rotation" },
216 { "-mw", FALSE, etBOOL, {&bMW},
217 "Use mass weighted fitting" }
227 char *grpname, title[256];
229 gmx_rmpbc_t gpbc = NULL;
233 const char *leg[] = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
234 #define NLEG asize(leg)
236 { efTRX, "-f", NULL, ffREAD },
237 { efTPS, NULL, NULL, ffREAD },
238 { efNDX, NULL, NULL, ffOPTRD },
239 { efXVG, NULL, "rotmat", ffWRITE }
241 #define NFILE asize(fnm)
243 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
244 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
249 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x_ref, NULL, box, bMW);
251 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
253 gmx_rmpbc(gpbc, top.atoms.nr, box, x_ref);
255 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
257 if (reffit[0][0] != 'n')
259 get_refx(oenv, ftp2fn(efTRX, NFILE, fnm), reffit[0][2] == 'z' ? 3 : 2, skip,
260 gnx, index, bMW, &top, ePBC, x_ref);
263 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
266 for (i = 0; i < gnx; i++)
268 if (index[i] >= natoms)
270 gmx_fatal(FARGS, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[i]+1, natoms);
272 w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
275 if (reffit[0][0] == 'n')
277 reset_x(gnx, index, natoms, NULL, x_ref, w_rls);
280 out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
281 "Fit matrix", "Time (ps)", "", oenv);
282 xvgr_legend(out, NLEG, leg, oenv);
286 gmx_rmpbc(gpbc, natoms, box, x);
288 reset_x(gnx, index, natoms, NULL, x, w_rls);
292 do_fit_ndim(2, natoms, w_rls, x_ref, x);
295 calc_fit_R(DIM, natoms, w_rls, x_ref, x, R);
298 "%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
300 R[XX][XX], R[XX][YY], R[XX][ZZ],
301 R[YY][XX], R[YY][YY], R[YY][ZZ],
302 R[ZZ][XX], R[ZZ][YY], R[ZZ][ZZ]);
304 while (read_next_x(oenv, status, &t, x, box));
306 gmx_rmpbc_done(gpbc);
312 do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");