On 2012-11-24 05:41, Acoot Brett wrote:
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?
In practice there is no problem to have a number of gromacs versions
installed. It is typically not recommended to switch gromacs versions of
mdrun during a project - unless there are know issues - but for the
analysis this is less critical. In this case 4.5.5 should be used.
Cheers,
Acoot
--- On Sat, 24/11/12, Justin Lemkul <jalem...@vt.edu> wrote:
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] Different average H bonds with different g_hbond
releases
To: "Discussion list for GROMACS users" <gmx-users@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
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 <er...@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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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