[gmx-users] g_hbond not running

[Erik Marklund]

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.

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