From 4459cfffe6b23c84b1e54cb45304a56ca3a4ae3b Mon Sep 17 00:00:00 2001 From: Justin Lemkul Date: Tue, 8 Oct 2013 07:38:04 -0400 Subject: [PATCH] Improvements to the g_lie help description. 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 --- src/tools/gmx_lie.c | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/tools/gmx_lie.c b/src/tools/gmx_lie.c index 3b5fd3bb95..98a902a901 100644 --- a/src/tools/gmx_lie.c +++ b/src/tools/gmx_lie.c @@ -145,8 +145,13 @@ int gmx_lie(int argc, char *argv[]) { 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"; @@ -190,6 +195,7 @@ int gmx_lie(int argc, char *argv[]) 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)) -- 2.22.0