[gmx-users] g_hbond not running

[antoni borysik]

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
> To: 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>>
>  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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