[gmx-users] Different average H bonds with different g_hbond releases

Justin Lemkul jalemkul at vt.edu
Fri Nov 23 23:30:53 CET 2012

On 11/23/12 5:23 PM, Luigi CAVALLO wrote:
> Hi,
> we have a .xtc and .tpr file. We were interested in the
> average number of H-bonds in the last 10ns of a 60ns long trajectory. We
> analyzed the jobs as g_hbond -f traj1_0-60ns.xtc -s topol.tpr -b 50000
> -num hbond.xvg. We are displaced by having a different number depending
> on the g_hbond release.
> Release 4.5.4 : Average number of hbonds per
> timeframe 163.620 out of 118112 possible
> Release 4.5.5 : Average
> number of hbonds per timeframe 168.168 out of 118112 possible
> Looking
> at the hbond.xvg file, the number of H-bonds in each frame are clearly
> different between the two releases. How is this possible ? We checked
> single versus double precision g_hbonds, same behavior. We checked that
> the initial part of the output, i.e. all the various g_hbond defaults,
> they are the same. We tested different computers and compilations, same
> behavior.
> The topology and the md run were done with release 4.5.4 if
> this could be a relevant information.

There was a bug that was fixed in May 2011 wherein 4.5.4 reported too few 
hydrogen bonds.

commit 91a481fad7ef0d87a4f8b2cb633c9dc40644350c
Author: Erik Marklund <erikm at anfinsen.bmc.uu.se>
Date:   Tue May 10 14:37:10 2011 +0200

     Fixed long standing bug where the merging resulted in too few hbonds.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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