[gmx-users] (no subject)

Gregory Man Kai Poon gpoon at gsu.edu
Thu Dec 1 13:24:47 CET 2016

Hi all:

I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated hydrogen bonding between two objects simulated in water.  The GROMACS manual discusses this in a Figure (9.8) - "water insertion". There is nothing in the online documentation as to how this should be done except a single mention with the -hbm option, which I tried.  It generated .xpm files such as the one attached.  They open, as far as I can tell, a very vertically compressed plot which I can make nothing out of.  Attempts to convert them to eps using xpm2eps output similar results.

So my questions are two-fold: 1) What is happening with the .xpm files?  2) Am I using the correct hbond option to enumerate water-mediated hydrogen bonds?

Many thanks in advance,





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