[gmx-users] Different average H bonds with different g_hbond releases
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 5 -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. Thanks, Luigi -- gmx-users mailing listgmx-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
Re: [gmx-users] Different average H bonds with different g_hbond releases
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 5 -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 listgmx-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
Re: [gmx-users] Different average H bonds with different g_hbond releases
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 5 -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 listgmx-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
Re: [gmx-users] Different average H bonds with different g_hbond releases
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 5 -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 listgmx-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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
