Information was sparse, likely to avoid restating published
protocols, but some expansion was definitely warranted,
given the amount of questions that have recently been
posted to the mailing list and Redmine.
Refs #1353
Change-Id: Ib4057ae671ccac70061498b1d40ebcba84c497ee
{
const char *desc[] = {
"[TT]g_lie[tt] computes a free energy estimate based on an energy analysis",
{
const char *desc[] = {
"[TT]g_lie[tt] 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."
+ "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 [TT].edr[tt] 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";
};
static real lie_lj = 0, lie_qq = 0, fac_lj = 0.181, fac_qq = 0.5;
static const char *ligand = "none";
ld = analyze_names(nre, enm, ligand);
snew(fr, 1);
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))
out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate",
"Time (ps)", "DGbind (kJ/mol)", oenv);
while (do_enx(fp, fr))