Hi, There’s an issue with g_hbond assuming periodic boundary conditions. I will try to fix this.
Kind regards, Erik > On 17 Dec 2014, at 12:05, Erik Marklund <erik.markl...@chem.ox.ac.uk> wrote: > > Hi Toni, > > Or better still, you can file a redmine issue and upload the files there: > http://redmine.gromacs.org. It facilitates bugfixing and makes sure it's not > forgotten. > > Erik > > On 17 Dec 2014, at 09:26, antoni borysik > <bory...@hotmail.co.uk<mailto:bory...@hotmail.co.uk>> wrote: > > > > will do thanks a lot. > Toni > > From: erik.markl...@chem.ox.ac.uk<mailto:erik.markl...@chem.ox.ac.uk> > To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> > Date: Wed, 17 Dec 2014 09:15:41 +0000 > Subject: Re: [gmx-users] g_hbond not running > > Hi Tony, > > Would you mind sending me the tpr and trr off list so I can have a closer > look and maybe debug? > > Erik > > On 17 Dec 2014, at 09:10, antoni borysik > <bory...@hotmail.co.uk<mailto:bory...@hotmail.co.uk>> wrote: > > > Hi Erik - yes tried that and no luck. g_hbond runs well with with some > simulation but not others. Can't figure it out, or why no-one has come across > this one before. > > > > From: erik.markl...@chem.ox.ac.uk<mailto:erik.markl...@chem.ox.ac.uk> > To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> > Date: Tue, 16 Dec 2014 14:50:15 +0000 > Subject: Re: [gmx-users] g_hbond not running > > Hi Toni, > > Have you tried with -nthreads 1, which effectively turns off the parallel > grid search? Never seen/heard of this problem before. > > Kind regards, > Erik > > > Erik Marklund, PhD > Postdoctoral Research Fellow, Fulford JRF > > Department of Chemistry > Physical & Theoretical Chemistry Laboratory > University of Oxford > South Parks Road > Oxford > OX1 3QZ > > On 16 Dec 2014, at 14:11, antoni borysik > <bory...@hotmail.co.uk<mailto:bory...@hotmail.co.uk><mailto:bory...@hotmail.co.uk>> > wrote: > > Hi, have run various vacuum simulations with GROMACS 4.6.7. I find I can > calculate h-bonds using g_hbond -f md.trr -s md.tpr on some simulations just > fine while on others the system freezes 'Frame loop parallelized with OpenMP > using 32 threads' even after leaving > 12 hours there is no progress or > error. I have not found this problem on the web nor been able to sort out > myself -> any insight would be most appreciated. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to > gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org><mailto:gmx-users-requ...@gromacs.org>. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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