[gmx-users] g_hbond not running

[Erik Marklund]

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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