[gmx-users] g_hbond not running

[Erik Marklund]

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.marklund at 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 <borysik at hotmail.co.uk<mailto:borysik at hotmail.co.uk>> wrote:
> 
> 
> 
> will do thanks a lot.
> Toni
> 
> From: erik.marklund at chem.ox.ac.uk<mailto:erik.marklund at chem.ox.ac.uk>
> To: gmx-users at gromacs.org<mailto:gmx-users at 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 <borysik at hotmail.co.uk<mailto:borysik at 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.marklund at chem.ox.ac.uk<mailto:erik.marklund at chem.ox.ac.uk>
> To: gmx-users at gromacs.org<mailto:gmx-users at 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 <borysik at hotmail.co.uk<mailto:borysik at hotmail.co.uk><mailto:borysik at 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-request at gromacs.org<mailto:gmx-users-request at gromacs.org><mailto:gmx-users-request at 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? 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-request at gromacs.org<mailto:gmx-users-request at 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? 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-request at gromacs.org<mailto:gmx-users-request at 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? 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-request at gromacs.org<mailto:gmx-users-request at 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? 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-request at gromacs.org<mailto:gmx-users-request at 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? 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-request at gromacs.org.