int gmx_lie(int argc,char *argv[])
{
const char *desc[] = {
"g_lie computes a free energy estimate based on an energy analysis",
"from. One needs an energy file with the following components:",
"Coul (A-B) LJ-SR (A-B) etc."
};
static real lie_lj=0,lie_qq=0,fac_lj=0.181,fac_qq=0.5;
static const char *ligand="none";
t_pargs pa[] = {
{ "-Elj", FALSE, etREAL, {&lie_lj},
"Lennard-Jones interaction between ligand and solvent" },
{ "-Eqq", FALSE, etREAL, {&lie_qq},
"Coulomb interaction between ligand and solvent" },
{ "-Clj", FALSE, etREAL, {&fac_lj},
"Factor in the LIE equation for Lennard-Jones component of energy" },
{ "-Cqq", FALSE, etREAL, {&fac_qq},
"Factor in the LIE equation for Coulomb component of energy" },
{ "-ligand", FALSE, etSTR, {&ligand},
"Name of the ligand in the energy file" }
};
#define NPA asize(pa)
FILE *out;
int nre,nframes=0,ct=0;
ener_file_t fp;
gmx_bool bCont;
t_liedata *ld;
gmx_enxnm_t *enm=NULL;
t_enxframe *fr;
real lie;
double lieaver=0,lieav2=0;
output_env_t oenv;
t_filenm fnm[] = {
{ efEDR, "-f", "ener", ffREAD },
{ efXVG, "-o", "lie", ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL,&oenv);
fp = open_enx(ftp2fn(efEDR,NFILE,fnm),"r");
do_enxnms(fp,&nre,&enm);
ld = analyze_names(nre,enm,ligand);
snew(fr,1);
out = xvgropen(ftp2fn(efXVG,NFILE,fnm),"LIE free energy estimate",
"Time (ps)","DGbind (kJ/mol)",oenv);
do {
bCont = do_enx(fp,fr);
ct = check_times(fr->t);
if (ct == 0) {
lie = calc_lie(ld,fr->ener,lie_lj,lie_qq,fac_lj,fac_qq);
lieaver += lie;
lieav2 += lie*lie;
nframes ++;
fprintf(out,"%10g %10g\n",fr->t,lie);
}
} while (bCont);
close_enx(fp);
ffclose(out);
fprintf(stderr,"\n");
if (nframes > 0)
printf("DGbind = %.3f (%.3f)\n",lieaver/nframes,
sqrt(lieav2/nframes-sqr(lieaver/nframes)));
do_view(oenv,ftp2fn(efXVG,NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}
int gmx_lie(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes a free energy estimate based on an energy analysis",
"from nonbonded energies. One needs an energy file with the following components:",
"Coul-(A-B) LJ-SR (A-B) etc.[PAR]",
"To utilize [TT]g_lie[tt] correctly, two simulations are required: one with the",
"molecule of interest bound to its receptor and one with the molecule in water.",
"Both need to utilize [TT]energygrps[tt] such that Coul-SR(A-B), LJ-SR(A-B), etc. terms",
"are written to the [REF].edr[ref] file. Values from the molecule-in-water simulation",
"are necessary for supplying suitable values for -Elj and -Eqq."
};
static real lie_lj = 0, lie_qq = 0, fac_lj = 0.181, fac_qq = 0.5;
static const char *ligand = "none";
t_pargs pa[] = {
{ "-Elj", FALSE, etREAL, {&lie_lj},
"Lennard-Jones interaction between ligand and solvent" },
{ "-Eqq", FALSE, etREAL, {&lie_qq},
"Coulomb interaction between ligand and solvent" },
{ "-Clj", FALSE, etREAL, {&fac_lj},
"Factor in the LIE equation for Lennard-Jones component of energy" },
{ "-Cqq", FALSE, etREAL, {&fac_qq},
"Factor in the LIE equation for Coulomb component of energy" },
{ "-ligand", FALSE, etSTR, {&ligand},
"Name of the ligand in the energy file" }
};
#define NPA asize(pa)
FILE *out;
int nre, nframes = 0, ct = 0;
ener_file_t fp;
t_liedata *ld;
gmx_enxnm_t *enm = NULL;
t_enxframe *fr;
real lie;
double lieaver = 0, lieav2 = 0;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
{ efEDR, "-f", "ener", ffREAD },
{ efXVG, "-o", "lie", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
fp = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
do_enxnms(fp, &nre, &enm);
ld = analyze_names(nre, enm, ligand);
snew(fr, 1);
out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate",
"Time (ps)", "DGbind (kJ/mol)", oenv);
while (do_enx(fp, fr))
{
ct = check_times(fr->t);
if (ct == 0)
{
lie = calc_lie(ld, fr->ener, lie_lj, lie_qq, fac_lj, fac_qq);
lieaver += lie;
lieav2 += lie*lie;
nframes++;
fprintf(out, "%10g %10g\n", fr->t, lie);
}
}
close_enx(fp);
xvgrclose(out);
fprintf(stderr, "\n");
if (nframes > 0)
{
printf("DGbind = %.3f (%.3f)\n", lieaver/nframes,
std::sqrt(lieav2/nframes-sqr(lieaver/nframes)));
}
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
return 0;
}
