[gmx-users] g_hbond not running

Erik Marklund erik.marklund at chem.ox.ac.uk
Tue Dec 16 15:50:19 CET 2014

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 Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

On 16 Dec 2014, at 14:11, antoni borysik <borysik at hotmail.co.uk<mailto:borysik at hotmail.co.uk>>

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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