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67 static int ocomp(const void *a, const void *b)
84 int gmx_trjorder(int argc, char *argv[])
86 const char *desc[] = {
87 "[TT]trjorder[tt] orders molecules according to the smallest distance",
88 "to atoms in a reference group",
89 "or on z-coordinate (with option [TT]-z[tt]).",
90 "With distance ordering, it will ask for a group of reference",
91 "atoms and a group of molecules. For each frame of the trajectory",
92 "the selected molecules will be reordered according to the shortest",
93 "distance between atom number [TT]-da[tt] in the molecule and all the",
94 "atoms in the reference group. The center of mass of the molecules can",
95 "be used instead of a reference atom by setting [TT]-da[tt] to 0.",
96 "All atoms in the trajectory are written",
97 "to the output trajectory.[PAR]",
98 "[TT]trjorder[tt] can be useful for e.g. analyzing the n waters closest to a",
100 "In that case the reference group would be the protein and the group",
101 "of molecules would consist of all the water atoms. When an index group",
102 "of the first n waters is made, the ordered trajectory can be used",
103 "with any Gromacs program to analyze the n closest waters.",
105 "If the output file is a [TT].pdb[tt] file, the distance to the reference target",
106 "will be stored in the B-factor field in order to color with e.g. Rasmol.",
108 "With option [TT]-nshell[tt] the number of molecules within a shell",
109 "of radius [TT]-r[tt] around the reference group are printed."
111 static int na = 3, ref_a = 1;
112 static real rcut = 0;
113 static gmx_bool bCOM = FALSE, bZ = FALSE;
115 { "-na", FALSE, etINT, {&na},
116 "Number of atoms in a molecule" },
117 { "-da", FALSE, etINT, {&ref_a},
118 "Atom used for the distance calculation, 0 is COM" },
119 { "-com", FALSE, etBOOL, {&bCOM},
120 "Use the distance to the center of mass of the reference group" },
121 { "-r", FALSE, etREAL, {&rcut},
122 "Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein" },
123 { "-z", FALSE, etBOOL, {&bZ},
124 "Order molecules on z-coordinate" }
129 gmx_bool bNShell, bPDBout;
132 rvec *x, *xsol, xcom, dx;
136 real t, totmass, mass, rcut2 = 0, n2;
137 int natoms, nwat, ncut;
138 char **grpname, title[256];
139 int i, j, d, *isize, isize_ref = 0, isize_sol;
140 atom_id sa, sr, *swi, **index, *ind_ref = NULL, *ind_sol;
143 { efTRX, "-f", NULL, ffREAD },
144 { efTPS, NULL, NULL, ffREAD },
145 { efNDX, NULL, NULL, ffOPTRD },
146 { efTRO, "-o", "ordered", ffOPTWR },
147 { efXVG, "-nshell", "nshell", ffOPTWR }
149 #define NFILE asize(fnm)
151 parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
152 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
154 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, TRUE);
157 /* get index groups */
158 printf("Select %sa group of molecules to be ordered:\n",
159 bZ ? "" : "a group of reference atoms and ");
163 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bZ ? 1 : 2,
164 isize, index, grpname);
168 isize_ref = isize[0];
169 isize_sol = isize[1];
175 isize_sol = isize[0];
179 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
180 if (natoms > top.atoms.nr)
182 gmx_fatal(FARGS, "Number of atoms in the run input file is larger than in the trjactory");
184 for (i = 0; (i < 2); i++)
186 for (j = 0; (j < isize[i]); j++)
188 if (index[i][j] > natoms)
190 gmx_fatal(FARGS, "An atom number in group %s is larger than the number of atoms in the trajectory");
195 if ((isize_sol % na) != 0)
197 gmx_fatal(FARGS, "Number of atoms in the molecule group (%d) is not a multiple of na (%d)",
204 gmx_fatal(FARGS, "The reference atom can not be larger than the number of atoms in a molecule");
210 for (i = 0; (i < natoms); i++)
217 bNShell = ((opt2bSet("-nshell", NFILE, fnm)) ||
218 (opt2parg_bSet("-r", asize(pa), pa)));
223 fp = xvgropen(opt2fn("-nshell", NFILE, fnm), "Number of molecules",
224 "Time (ps)", "N", oenv);
225 printf("Will compute the number of molecules within a radius of %g\n",
228 if (!bNShell || opt2bSet("-o", NFILE, fnm))
230 bPDBout = (fn2ftp(opt2fn("-o", NFILE, fnm)) == efPDB);
231 if (bPDBout && !top.atoms.pdbinfo)
233 fprintf(stderr, "Creating pdbfino records\n");
234 snew(top.atoms.pdbinfo, top.atoms.nr);
236 out = open_trx(opt2fn("-o", NFILE, fnm), "w");
238 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms, box);
241 gmx_rmpbc(gpbc, natoms, box, x);
242 set_pbc(&pbc, ePBC, box);
246 /* Calculate the COM of all solvent molecules */
247 for (i = 0; i < nwat; i++)
251 for (j = 0; j < na; j++)
253 sa = ind_sol[i*na+j];
254 mass = top.atoms.atom[sa].m;
256 for (d = 0; d < DIM; d++)
258 xsol[i][d] += mass*x[sa][d];
261 svmul(1/totmass, xsol[i], xsol[i]);
266 /* Copy the reference atom of all solvent molecules */
267 for (i = 0; i < nwat; i++)
269 copy_rvec(x[ind_sol[i*na+ref_a]], xsol[i]);
275 for (i = 0; (i < nwat); i++)
279 order[i].d2 = xsol[i][ZZ];
286 for (i = 0; i < isize_ref; i++)
288 mass = top.atoms.atom[ind_ref[i]].m;
290 for (j = 0; j < DIM; j++)
292 xcom[j] += mass*x[ind_ref[i]][j];
295 svmul(1/totmass, xcom, xcom);
296 for (i = 0; (i < nwat); i++)
299 pbc_dx(&pbc, xcom, xsol[i], dx);
301 order[i].d2 = norm2(dx);
306 /* Set distance to first atom */
307 for (i = 0; (i < nwat); i++)
310 pbc_dx(&pbc, x[ind_ref[0]], xsol[i], dx);
312 order[i].d2 = norm2(dx);
314 for (j = 1; (j < isize_ref); j++)
317 for (i = 0; (i < nwat); i++)
320 pbc_dx(&pbc, x[sr], xsol[i], dx);
322 if (n2 < order[i].d2)
333 for (i = 0; (i < nwat); i++)
335 if (order[i].d2 <= rcut2)
340 fprintf(fp, "%10.3f %8d\n", t, ncut);
344 qsort(order, nwat, sizeof(*order), ocomp);
345 for (i = 0; (i < nwat); i++)
347 for (j = 0; (j < na); j++)
349 swi[ind_sol[na*i]+j] = order[i].i+j;
353 /* Store the distance as the B-factor */
356 for (i = 0; (i < nwat); i++)
358 for (j = 0; (j < na); j++)
360 top.atoms.pdbinfo[order[i].i+j].bfac = sqrt(order[i].d2);
364 write_trx(out, natoms, swi, &top.atoms, 0, t, box, x, NULL, NULL);
367 while (read_next_x(oenv, status, &t, natoms, x, box));
377 gmx_rmpbc_done(gpbc);