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
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
Universi
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 Rese
it out, or why no-one has come across
> this one before.
>
>
>
>> From: erik.markl...@chem.ox.ac.uk
>> To: gmx-us...@gromacs.org
>> Date: Tue, 16 Dec 2014 14:50:15 +0000
>> Subject: Re: [gmx-users] g_hbond not running
>>
>> Hi Toni,
>>
will do thanks a lot.
Toni
> From: erik.markl...@chem.ox.ac.uk
> To: gmx-us...@gromacs.org
> Date: Wed, 17 Dec 2014 09:15:41 +
> 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
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 +
Subject: Re: [gmx-users] g_hbond not running
Hi Tony,
Would you mind sending me the tpr and trr off list so I can
c.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 +
> Subject: Re: [gmx-users] g_hbond not running
>
> Hi Tony,
>
> Would you mind sending me the tpr and trr off list so
