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?
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 > -- 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
