[gmx-users] hbond

Justin Lemkul jalemkul at vt.edu
Fri Dec 2 13:47:29 CET 2016

On 12/1/16 10:58 AM, Gregory Poon wrote:
> On 12/1/2016 7:45 AM, Justin Lemkul wrote:
>> 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
> Thanks for your comments, Justin.  When I invoke hbond by:
> gmx hbond -f *.xtc -s *.tpr -num -hbn -g (± other options)
> I get hbnum which shows changes with respect with time, but the hbond.ndx and
> hbond.log files have no time information.  Are they averages of some sort?  Or a
> particular frame that it defaults to? If so, how do I specific the frames/times?

Asking for -hbn requires -hbm to be useful.  The index file produced is the key 
for what the hydrogen bonds are in the .xpm file from -hbm.



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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