Look at the top of the output of any GROMACS program. Mark
On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett <acootbr...@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 <sp...@xray.bmc.uu.se> wrote: > > > From: David van der Spoel <sp...@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@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 <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 > > >> > > >> ======================================== > > >> -- > > >> gmx-users mailing list gmx-users@gromacs.org > > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > > >> before posting! > > >> * Please don't post (un)subscribe requests to the > > list. Use > > >> the > > >> www interface or send it to gmx-users-requ...@gromacs.org. > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > > Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: > > +46184714205. > > sp...@xray.bmc.uu.se > > http://folding.bmc.uu.se > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > > before posting! > > * Please don't post (un)subscribe requests to the list. Use > > the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
