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48 #include "gmx_fatal.h"
51 static real dointerp(int n, rvec x1[], rvec x2[], rvec xx[],
52 int I, int N, real first, real last)
55 double fac, fac0, fac1;
57 fac = first + (I*(last-first))/(N-1);
60 for (i = 0; (i < n); i++)
62 for (j = 0; (j < DIM); j++)
64 xx[i][j] = fac0*x1[i][j] + fac1*x2[i][j];
71 int gmx_morph(int argc, char *argv[])
73 const char *desc[] = {
74 "[TT]g_morph[tt] does a linear interpolation of conformations in order to",
75 "create intermediates. Of course these are completely unphysical, but",
76 "that you may try to justify yourself. Output is in the form of a ",
77 "generic trajectory. The number of intermediates can be controlled with",
78 "the [TT]-ninterm[tt] flag. The first and last flag correspond to the way of",
79 "interpolating: 0 corresponds to input structure 1 while",
80 "1 corresponds to input structure 2.",
81 "If you specify [TT]-first[tt] < 0 or [TT]-last[tt] > 1 extrapolation will be",
82 "on the path from input structure x[SUB]1[sub] to x[SUB]2[sub]. In general, the coordinates",
83 "of the intermediate x(i) out of N total intermediates correspond to:[PAR]",
84 "x(i) = x[SUB]1[sub] + (first+(i/(N-1))*(last-first))*(x[SUB]2[sub]-x[SUB]1[sub])[PAR]",
85 "Finally the RMSD with respect to both input structures can be computed",
86 "if explicitly selected ([TT]-or[tt] option). In that case, an index file may be",
87 "read to select the group from which the RMS is computed."
90 { efSTX, "-f1", "conf1", ffREAD },
91 { efSTX, "-f2", "conf2", ffREAD },
92 { efTRX, "-o", "interm", ffWRITE },
93 { efXVG, "-or", "rms-interm", ffOPTWR },
94 { efNDX, "-n", "index", ffOPTRD }
96 #define NFILE asize(fnm)
97 static int ninterm = 11;
98 static real first = 0.0;
99 static real last = 1.0;
100 static gmx_bool bFit = TRUE;
102 { "-ninterm", FALSE, etINT, {&ninterm},
103 "Number of intermediates" },
104 { "-first", FALSE, etREAL, {&first},
105 "Corresponds to first generated structure (0 is input x[SUB]1[sub], see above)" },
106 { "-last", FALSE, etREAL, {&last},
107 "Corresponds to last generated structure (1 is input x[SUB]2[sub], see above)" },
108 { "-fit", FALSE, etBOOL, {&bFit},
109 "Do a least squares fit of the second to the first structure before interpolating" }
111 const char *leg[] = { "Ref = 1\\Sst\\N conf", "Ref = 2\\Snd\\N conf" };
113 int i, isize, is_lsq, nat1, nat2;
115 atom_id *index, *index_lsq, *index_all, *dummy;
117 rvec *x1, *x2, *xx, *v;
119 real rms1, rms2, fac, *mass;
120 char title[STRLEN], *grpname;
124 parse_common_args(&argc, argv, PCA_CAN_VIEW,
125 NFILE, fnm, asize(pa), pa, asize(desc), desc,
127 get_stx_coordnum (opt2fn("-f1", NFILE, fnm), &nat1);
128 get_stx_coordnum (opt2fn("-f2", NFILE, fnm), &nat2);
131 gmx_fatal(FARGS, "Number of atoms in first structure is %d, in second %d",
135 init_t_atoms(&atoms, nat1, TRUE);
141 read_stx_conf(opt2fn("-f1", NFILE, fnm), title, &atoms, x1, v, NULL, box);
142 read_stx_conf(opt2fn("-f2", NFILE, fnm), title, &atoms, x2, v, NULL, box);
145 snew(index_all, nat1);
146 for (i = 0; (i < nat1); i++)
153 printf("Select group for LSQ superposition:\n");
154 get_index(&atoms, opt2fn_null("-n", NFILE, fnm), 1, &is_lsq, &index_lsq,
156 reset_x(is_lsq, index_lsq, nat1, index_all, x1, mass);
157 reset_x(is_lsq, index_lsq, nat1, index_all, x2, mass);
158 do_fit(nat1, mass, x1, x2);
161 bRMS = opt2bSet("-or", NFILE, fnm);
164 fp = xvgropen(opt2fn("-or", NFILE, fnm), "RMSD", "Conf", "(nm)", oenv);
165 xvgr_legend(fp, asize(leg), leg, oenv);
166 printf("Select group for RMSD calculation:\n");
167 get_index(&atoms, opt2fn_null("-n", NFILE, fnm), 1, &isize, &index, &grpname);
168 printf("You selected group %s, containing %d atoms\n", grpname, isize);
169 rms1 = rmsdev_ind(isize, index, mass, x1, x2);
170 fprintf(stderr, "RMSD between input conformations is %g nm\n", rms1);
174 for (i = 0; (i < nat1); i++)
178 status = open_trx(ftp2fn(efTRX, NFILE, fnm), "w");
180 for (i = 0; (i < ninterm); i++)
182 fac = dointerp(nat1, x1, x2, xx, i, ninterm, first, last);
183 write_trx(status, nat1, dummy, &atoms, i, fac, box, xx, NULL, NULL);
186 rms1 = rmsdev_ind(isize, index, mass, x1, xx);
187 rms2 = rmsdev_ind(isize, index, mass, x2, xx);
188 fprintf(fp, "%10g %10g %10g\n", fac, rms1, rms2);
197 do_view(oenv, opt2fn("-or", NFILE, fnm), "-nxy");