From: Justin Lemkul <jalemkul@vt.edu>
Date: Tue, 8 Oct 2013 11:38:04 +0000 (-0400)
Subject: Improvements to the g_lie help description.
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=4459cfffe6b23c84b1e54cb45304a56ca3a4ae3b;p=alexxy%2Fgromacs.git

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
---

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))