[gmx-users] Different average H bonds with different g_hbond releases
David van der Spoel
spoel at xray.bmc.uu.se
Sat Nov 24 07:30:44 CET 2012
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.
> --- 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:
>>> 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
>>> 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
>>> 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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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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