On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote:
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.


You can use an .m2p file to adjust the sizes of the x- and y-axes to make it legible. The real value is in the data within, though. You have to map the actual participating groups (the output of of -hbn) with the individual time series in the .xpm from -hbm.


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?


To actually analyze water-mediated H-bonds requires additional work that GROMACS tools don't do. You need to analyze water H-bonds with the two groups of interest separately, then determine if the same water is H-bonded to a moiety in both of those groups in the same frame. This is where tracing the H-bonds in the .xpm file is useful.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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