[gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5

[Mark Abraham]

Look at the top of the output of any GROMACS program.

Mark

On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett <acootbrett at yahoo.com> wrote:

> Dear All,
>
> Is any gromacs command which can tell us or distinguish whether what
> installed is gromacs 4.5.4 or 4.5.5?
>
> Cheers,
>
> Acoot
>
>
> --- On Sat, 24/11/12, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > 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, 5:30 PM
> > 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 <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
> > >> 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
> > >>
> > >> --
> > >> ========================================
> > >>
> > >> 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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> > >>
> >
> >
> > --
> > 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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