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

[Szilárd Páll]

Or run any binary with the -version option e.g:
$ mdrun -version

--
Szilárd


On Sun, Nov 25, 2012 at 10:30 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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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