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49 #include "gmx_fatal.h"
67 static t_liedata *analyze_names(int nre,gmx_enxnm_t *names,const char *ligand)
73 /* Skip until we come to pressure */
74 for(i=0; (i<F_NRE); i++)
75 if (strcmp(names[i].name,interaction_function[F_PRES].longname) == 0)
78 /* Now real analysis: find components of energies */
79 sprintf(self,"%s-%s",ligand,ligand);
81 for( ; (i<nre); i++) {
82 if ((strstr(names[i].name,ligand) != NULL) &&
83 (strstr(names[i].name,self) == NULL)) {
84 if (strstr(names[i].name,"LJ") != NULL) {
86 srenew(ld->lj,ld->nlj);
87 ld->lj[ld->nlj-1] = i;
89 else if (strstr(names[i].name,"Coul") != NULL) {
91 srenew(ld->qq,ld->nqq);
92 ld->qq[ld->nqq-1] = i;
96 printf("Using the following energy terms:\n");
98 for(i=0; (i<ld->nlj); i++)
99 printf(" %12s",names[ld->lj[i]].name);
101 for(i=0; (i<ld->nqq); i++)
102 printf(" %12s",names[ld->qq[i]].name);
108 real calc_lie(t_liedata *ld,t_energy ee[],real lie_lj,real lie_qq,
109 real fac_lj,real fac_qq)
115 for(i=0; (i<ld->nlj); i++)
116 lj_tot += ee[ld->lj[i]].e;
118 for(i=0; (i<ld->nqq); i++)
119 qq_tot += ee[ld->qq[i]].e;
121 /* And now the great LIE formula: */
122 return fac_lj*(lj_tot-lie_lj)+fac_qq*(qq_tot-lie_qq);
125 int gmx_lie(int argc,char *argv[])
127 const char *desc[] = {
128 "g_lie computes a free energy estimate based on an energy analysis",
129 "from. One needs an energy file with the following components:",
130 "Coul (A-B) LJ-SR (A-B) etc."
132 static real lie_lj=0,lie_qq=0,fac_lj=0.181,fac_qq=0.5;
133 static const char *ligand="none";
135 { "-Elj", FALSE, etREAL, {&lie_lj},
136 "Lennard-Jones interaction between ligand and solvent" },
137 { "-Eqq", FALSE, etREAL, {&lie_qq},
138 "Coulomb interaction between ligand and solvent" },
139 { "-Clj", FALSE, etREAL, {&fac_lj},
140 "Factor in the LIE equation for Lennard-Jones component of energy" },
141 { "-Cqq", FALSE, etREAL, {&fac_qq},
142 "Factor in the LIE equation for Coulomb component of energy" },
143 { "-ligand", FALSE, etSTR, {&ligand},
144 "Name of the ligand in the energy file" }
146 #define NPA asize(pa)
149 int nre,nframes=0,ct=0;
153 gmx_enxnm_t *enm=NULL;
156 double lieaver=0,lieav2=0;
160 { efEDR, "-f", "ener", ffREAD },
161 { efXVG, "-o", "lie", ffWRITE }
163 #define NFILE asize(fnm)
165 CopyRight(stderr,argv[0]);
166 parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
167 NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL,&oenv);
169 fp = open_enx(ftp2fn(efEDR,NFILE,fnm),"r");
170 do_enxnms(fp,&nre,&enm);
172 ld = analyze_names(nre,enm,ligand);
174 out = xvgropen(ftp2fn(efXVG,NFILE,fnm),"LIE free energy estimate",
175 "Time (ps)","DGbind (kJ/mol)",oenv);
177 bCont = do_enx(fp,fr);
178 ct = check_times(fr->t);
180 lie = calc_lie(ld,fr->ener,lie_lj,lie_qq,fac_lj,fac_qq);
184 fprintf(out,"%10g %10g\n",fr->t,lie);
189 fprintf(stderr,"\n");
192 printf("DGbind = %.3f (%.3f)\n",lieaver/nframes,
193 sqrt(lieav2/nframes-sqr(lieaver/nframes)));
195 do_view(oenv,ftp2fn(efXVG,NFILE,fnm),"-nxy");