3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
11 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
12 * Copyright (c) 2001-2004, The GROMACS development team,
13 * check out http://www.gromacs.org for more information.
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
17 * as published by the Free Software Foundation; either version 2
18 * of the License, or (at your option) any later version.
20 * If you want to redistribute modifications, please consider that
21 * scientific software is very special. Version control is crucial -
22 * bugs must be traceable. We will be happy to consider code for
23 * inclusion in the official distribution, but derived work must not
24 * be called official GROMACS. Details are found in the README & COPYING
25 * files - if they are missing, get the official version at www.gromacs.org.
27 * To help us fund GROMACS development, we humbly ask that you cite
28 * the papers on the package - you can find them in the top README file.
30 * For more info, check our website at http://www.gromacs.org
33 * Green Red Orange Magenta Azure Cyan Skyblue
56 static void dump_dih(int nframes,char *title,real time[],real dih[])
62 sprintf(fname,"dih.%s",title);
63 printf("A dihedral transition occurred in %s\n",fname);
64 printf("Do you want to plot it to %s ? (y/n) ",fname);
66 out=ffopen(fname,"w");
67 for(i=0; (i<nframes); i++)
68 fprintf(out,"%10.3f %12.5e\n",time[i],dih[i]);
72 static void ana_dih(FILE *out,char *index,int nframes,real dih[],t_dih *dd)
75 real mind,maxd,sum,av,var,prev,width;
78 mind=5400,maxd=-5400,sum=0,av=0,var=0;
81 for(i=0; (i<nframes); i++) {
82 if ((dih[i]-prev) > 180) {
86 else if ((dih[i]-prev) < -180)
91 mind=min(mind,dih[i]);
92 maxd=max(maxd,dih[i]);
95 for(i=0; (i<nframes); i++)
98 width=(360.0/dd->mult);
99 bTrans=((maxd - mind) > width);
101 fprintf(out,"%-10s %10.3f %10.3f %10.3f %10.3f %10.3f %-10s%3.0f\n",
102 index,mind,av,maxd,var,sqrt(var),
103 bTrans ? "Yep" : "",width);
106 static int find_min(real phi,int ntab,real phitab[])
112 /* Set closest minimum to the first one */
114 mind=fabs(phi-phitab[0]);
116 for(i=1; (i<ntab); i++) {
117 mm=fabs(phi-phitab[i]);
123 if (mind < width*0.5 )
129 static int vphi(t_dih *dih,real phi,int mult)
131 static real m2[] = { 90, 270 };
132 static real m3[] = { 60, 180, 300 };
133 static real m4[] = { 45, 135, 225, 315 };
134 static real m6[] = { 30, 90, 150, 210, 270, 330 };
139 phiref=RAD2DEG*(phi-dih->phi0);
147 vpp=find_min(phiref,2,m2);
150 vpp=find_min(phiref,3,m3);
153 vpp=find_min(phiref,4,m4);
156 vpp=find_min(phiref,6,m6);
159 gmx_fatal(FARGS,"No such multiplicity %d",dih->mult);
168 typedef struct t_cluster {
172 struct t_cluster *next;
175 static t_cluster *search_cluster(t_cluster *cl,char *minimum)
179 while (ccl != NULL) {
180 if (strcmp(minimum,ccl->minimum)==0)
187 static void add_cluster(t_cluster **cl,int ndih,char *minimum)
195 ccl->minimum=strdup(minimum);
202 while (loper->next != NULL)
208 static void p_cluster(FILE *out,t_cluster *cl)
212 fprintf(out,"* * * C L U S T E R A N A L Y S I S * * *\n\n");
213 fprintf(out," Frequency Dihedral minima\n");
215 while (loper != NULL) {
216 fprintf(out,"%10d %s\n",loper->freq,loper->minimum);
221 static void ana_cluster(FILE *out, t_xrama *xr,real **dih,real time[],
222 t_topology *top,int nframes,int mult)
224 t_cluster *cl=NULL,*scl;
228 /* Number of dihedrals + terminating NULL
229 * this allows for using string routines
231 snew(minimum,xr->ndih+1);
233 for(i=0; (i<nframes); i++) {
235 for(j=0; (j<xr->ndih); j++) {
236 minimum[j] = vphi(&xr->dih[j],dih[j][i],
237 mult == -1 ? xr->dih[j].mult : mult);
238 if (minimum[j] == NOMIN)
242 if ((scl=search_cluster(cl,minimum)) == NULL)
243 add_cluster(&cl,xr->ndih,minimum);
253 static void ana_trans(FILE *out, t_xrama *xr,real **dih,real time[],
254 t_topology *top,int nframes, const output_env_t oenv)
257 real prev_phi,prev_psi;
261 fprintf(out,"\n\t* * * D I H E D R A L S T A T I S T I C S * * *\n\n");
262 fprintf(out,"%-10s %10s %10s %10s %10s %10s %10s\n",
263 "index","minimum","average","maximum","variance","std.dev",
265 for(i=0; (i<xr->ndih); i++) {
266 sprintf(buf,"dih-%d",i);
267 ana_dih(out,buf,nframes,dih[i],&(xr->dih[i]));
269 for(i=0; (i<xr->npp); i++) {
270 sprintf(buf,"%s",xr->pp[i].label);
271 outd=xvgropen(buf,"Dihedral Angles","Time (ps)","Degrees",oenv);
275 prev_phi=dih[phi][0];
276 prev_psi=dih[psi][0];
277 for(j=0; (j<nframes); j++) {
279 if ((dih[phi][j]-prev_phi) > 180)
281 else if ((dih[phi][j]-prev_phi) < -180)
283 prev_phi=dih[phi][j];
284 if ((dih[psi][j]-prev_psi) > 180)
286 else if ((dih[psi][j]-prev_psi) < -180)
288 prev_psi=dih[psi][j];
289 fprintf(outd,"%10g %10g %10g\n",time[j],prev_phi,prev_psi);
295 int gmx_dih(int argc,char *argv[])
297 const char *desc[] = {
298 "g_dih can do two things. The default is to analyze dihedral transitions",
299 "by merely computing all the dihedral angles defined in your topology",
300 "for the whole trajectory. When a dihedral flips over to another minimum",
301 "an angle/time plot is made.[PAR]",
302 "The opther option is to discretize the dihedral space into a number of",
303 "bins, and group each conformation in dihedral space in the",
304 "appropriate bin. The output is then given as a number of dihedral",
305 "conformations sorted according to occupancy."
307 static int mult = -1;
308 static bool bSA = FALSE;
310 { "-sa", FALSE, etBOOL, {&bSA},
311 "Perform cluster analysis in dihedral space instead of analysing dihedral transitions." },
312 { "-mult", FALSE, etINT, {&mult},
313 "mulitiplicity for dihedral angles (by default read from topology)" }
320 int i,nframes,maxframes=1000;
323 { efTRX, "-f", NULL, ffREAD },
324 { efTPX, NULL, NULL, ffREAD },
325 { efOUT, NULL, NULL, ffWRITE }
327 #define NFILE asize(fnm)
329 CopyRight(stderr,argv[0]);
330 parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
331 NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
334 fprintf(stderr,"Using %d for dihedral multiplicity rather than topology values\n",mult);
337 init_rama(oenv,ftp2fn(efTRX,NFILE,fnm),
338 ftp2fn(efTPX,NFILE,fnm),xr,3);
339 top=read_top(ftp2fn(efTPX,NFILE,fnm),NULL);
341 /* Brute force malloc, may be too big... */
343 for(i=0; (i<xr->ndih); i++)
344 snew(dih[i],maxframes);
345 snew(time,maxframes);
347 fprintf(stderr,"\n");
349 while (new_data(xr)) {
350 for(i=0; (i<xr->ndih); i++) {
351 dd=xr->dih[i].ang*RAD2DEG;
360 if (nframes > maxframes) {
362 for(i=0; (i<xr->ndih); i++)
363 srenew(dih[i],maxframes);
364 srenew(time,maxframes);
368 fprintf(stderr,"\nCalculated all dihedrals, now analysing...\n");
370 out=ftp2FILE(efOUT,NFILE,fnm,"w");
373 /* Cluster and structure analysis */
374 ana_cluster(out,xr,dih,time,top,nframes,mult);
377 /* Analyse transitions... */
378 ana_trans(out,xr,dih,time,top,nframes,oenv);