[gmx-users] Different average H bonds with different g_hbond releases
acootbrett at yahoo.com
Sat Nov 24 05:41:16 CET 2012
If we got the results by 4.5.4, what will be the method to analyze it by 4.5.5? By a pathch or by installation of 4.5.5 to analyze the 4.5.4 results?
--- On Sat, 24/11/12, Justin Lemkul <jalemkul at vt.edu> wrote:
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Different average H bonds with different g_hbond releases
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Received: Saturday, 24 November, 2012, 9:30 AM
> On 11/23/12 5:23 PM, Luigi CAVALLO wrote:
> > Hi,
> > we have a .xtc and .tpr file. We were interested in
> > 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
> > 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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