Re: [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5
Or run any binary with the -version option e.g: $ mdrun -version -- Szilárd On Sun, Nov 25, 2012 at 10:30 AM, Mark Abraham wrote: > Look at the top of the output of any GROMACS program. > > Mark > > On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett > 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 wrote: > > > > > From: David van der Spoel > > > Subject: Re: [gmx-users] Different average H bonds with different > > g_hbond releases > > > To: "Discussion list for GROMACS users" > > > 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 > > > wrote: > > > > > > > >> From: Justin Lemkul > > > >> Subject: Re: [gmx-users] Different average H bonds > > > with different g_hbond releases > > > >> To: "Discussion list for GROMACS users" > > > >> 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 > > > >> 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.se > > > http://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
Re: [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5
Look at the top of the output of any GROMACS program. Mark On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett 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 wrote: > > > From: David van der Spoel > > Subject: Re: [gmx-users] Different average H bonds with different > g_hbond releases > > To: "Discussion list for GROMACS users" > > 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 > > wrote: > > > > > >> From: Justin Lemkul > > >> Subject: Re: [gmx-users] Different average H bonds > > with different g_hbond releases > > >> To: "Discussion list for GROMACS users" > > >> 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 > > >> 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.se > > http://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 > > > -- > 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://w
[gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5
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 wrote: > From: David van der Spoel > Subject: Re: [gmx-users] Different average H bonds with different g_hbond > releases > To: "Discussion list for GROMACS users" > 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 > wrote: > > > >> From: Justin Lemkul > >> Subject: Re: [gmx-users] Different average H bonds > with different g_hbond releases > >> To: "Discussion list for GROMACS users" > >> 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 > >> 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 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
