[gmx-users] g_hbond not running

[antoni borysik]

will do thanks a lot.
Toni

> From: erik.marklund at chem.ox.ac.uk
> To: 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> 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
> >> 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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