Expanded the help text regarding the -r2 and -ac options.

Fixes #862

Change-Id: If7ff131648881da8b1749bc736e141ff0b307ca6

diff --git a/src/tools/gmx_hbond.c b/src/tools/gmx_hbond.c
index 16c48812e7efd737069ec9b5e256a20ce0876aae..e0c77591a7a49a3ee630dc89a5603766d8f67af3 100644 (file)
--- a/src/tools/gmx_hbond.c
+++ b/src/tools/gmx_hbond.c
@@ -3049,6 +3049,15 @@ int gmx_hbond(int argc,char *argv[])
         "which should contain exactly one atom. In this case, only hydrogen",
         "bonds between atoms within the shell distance from the one atom are",
         "considered.[PAR]",
+
+        "With option -ac, rate constants for hydrogen bonding can be derived with the model of Luzar and Chandler",
+        "(Nature 394, 1996; J. Chem. Phys. 113:23, 2000) or that of Markovitz and Agmon (J. Chem. Phys 129, 2008).",
+        "If contact kinetics are analyzed by using the -contact option, then",
+        "n(t) can be defined as either all pairs that are not within contact distance r at time t",
+        "(corresponding to leaving the -r2 option at the default value 0) or all pairs that",
+        "are within distance r2 (corresponding to setting a second cut-off value with option -r2).",
+        "See mentioned literature for more details and definitions."
+        "[PAR]",
     
         /*    "It is also possible to analyse specific hydrogen bonds with",
               "[TT]-sel[tt]. This index file must contain a group of atom triplets",