Merge release-4-6 into release-5-0

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_lie.c

diff --git a/src/gromacs/gmxana/gmx_lie.c b/src/gromacs/gmxana/gmx_lie.c
index 3e29541e9eeda3cb426f9ed9e196542b02827d22..7a9a689cc833cbdc61704f12eba7ec0906dc57dd 100644 (file)
--- a/src/gromacs/gmxana/gmx_lie.c
+++ b/src/gromacs/gmxana/gmx_lie.c
@@ -141,8 +141,13 @@ int gmx_lie(int argc, char *argv[])
 {
     const char        *desc[] = {
         "[THISMODULE] 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";
@@ -188,6 +193,7 @@ 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))