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51 #include "gmx_fatal.h"
54 static real dointerp(int n,rvec x1[],rvec x2[],rvec xx[],
55 int I,int N,real first,real last)
60 fac = first + (I*(last-first))/(N-1);
64 for(j=0; (j<DIM); j++)
65 xx[i][j] = fac0*x1[i][j] + fac1*x2[i][j];
70 int gmx_morph(int argc,char *argv[])
72 const char *desc[] = {
73 "[TT]g_morph[tt] does a linear interpolation of conformations in order to",
74 "create intermediates. Of course these are completely unphysical, but",
75 "that you may try to justify yourself. Output is in the form of a ",
76 "generic trajectory. The number of intermediates can be controlled with",
77 "the [TT]-ninterm[tt] flag. The first and last flag correspond to the way of",
78 "interpolating: 0 corresponds to input structure 1 while",
79 "1 corresponds to input structure 2.",
80 "If you specify [TT]-first[tt] < 0 or [TT]-last[tt] > 1 extrapolation will be",
81 "on the path from input structure x[SUB]1[sub] to x[SUB]2[sub]. In general, the coordinates",
82 "of the intermediate x(i) out of N total intermediates correspond to:[PAR]",
83 "x(i) = x[SUB]1[sub] + (first+(i/(N-1))*(last-first))*(x[SUB]2[sub]-x[SUB]1[sub])[PAR]",
84 "Finally the RMSD with respect to both input structures can be computed",
85 "if explicitly selected ([TT]-or[tt] option). In that case, an index file may be",
86 "read to select the group from which the RMS is computed."
89 { efSTX, "-f1", "conf1", ffREAD },
90 { efSTX, "-f2", "conf2", ffREAD },
91 { efTRX, "-o", "interm", ffWRITE },
92 { efXVG, "-or", "rms-interm", ffOPTWR },
93 { efNDX, "-n", "index", ffOPTRD }
95 #define NFILE asize(fnm)
96 static int ninterm = 11;
97 static real first = 0.0;
98 static real last = 1.0;
99 static gmx_bool bFit = TRUE;
101 { "-ninterm", FALSE, etINT, {&ninterm},
102 "Number of intermediates" },
103 { "-first", FALSE, etREAL, {&first},
104 "Corresponds to first generated structure (0 is input x[SUB]1[sub], see above)" },
105 { "-last", FALSE, etREAL, {&last},
106 "Corresponds to last generated structure (1 is input x[SUB]2[sub], see above)" },
107 { "-fit", FALSE, etBOOL, {&bFit},
108 "Do a least squares fit of the second to the first structure before interpolating" }
110 const char *leg[] = { "Ref = 1\\Sst\\N conf", "Ref = 2\\Snd\\N conf" };
112 int i,isize,is_lsq,nat1,nat2;
114 atom_id *index,*index_lsq,*index_all,*dummy;
118 real rms1,rms2,fac,*mass;
119 char title[STRLEN],*grpname;
123 CopyRight(stderr,argv[0]);
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);
130 gmx_fatal(FARGS,"Number of atoms in first structure is %d, in second %d",
133 init_t_atoms(&atoms,nat1,TRUE);
139 read_stx_conf(opt2fn("-f1",NFILE,fnm),title,&atoms,x1,v,NULL,box);
140 read_stx_conf(opt2fn("-f2",NFILE,fnm),title,&atoms,x2,v,NULL,box);
143 snew(index_all,nat1);
144 for(i=0; (i<nat1); i++) {
149 printf("Select group for LSQ superposition:\n");
150 get_index(&atoms,opt2fn_null("-n",NFILE,fnm),1,&is_lsq,&index_lsq,
152 reset_x(is_lsq,index_lsq,nat1,index_all,x1,mass);
153 reset_x(is_lsq,index_lsq,nat1,index_all,x2,mass);
154 do_fit(nat1,mass,x1,x2);
157 bRMS = opt2bSet("-or",NFILE,fnm);
159 fp = xvgropen(opt2fn("-or",NFILE,fnm),"RMSD","Conf","(nm)",oenv);
160 xvgr_legend(fp,asize(leg),leg,oenv);
161 printf("Select group for RMSD calculation:\n");
162 get_index(&atoms,opt2fn_null("-n",NFILE,fnm),1,&isize,&index,&grpname);
163 printf("You selected group %s, containing %d atoms\n",grpname,isize);
164 rms1 = rmsdev_ind(isize,index,mass,x1,x2);
165 fprintf(stderr,"RMSD between input conformations is %g nm\n",rms1);
169 for(i=0; (i<nat1); i++)
171 status = open_trx(ftp2fn(efTRX,NFILE,fnm),"w");
173 for(i=0; (i<ninterm); i++) {
174 fac = dointerp(nat1,x1,x2,xx,i,ninterm,first,last);
175 write_trx(status,nat1,dummy,&atoms,i,fac,box,xx,NULL,NULL);
177 rms1 = rmsdev_ind(isize,index,mass,x1,xx);
178 rms2 = rmsdev_ind(isize,index,mass,x2,xx);
179 fprintf(fp,"%10g %10g %10g\n",fac,rms1,rms2);
187 do_view(oenv,opt2fn("-or",NFILE,fnm),"-nxy");