Problem is that I can not find out if gromacs (or MPI) is using the
resources correctly. Is there any idea to see if there is any bottleneck
for such low utilization?

Regards,
Mahmood



On Mon, Oct 17, 2016 at 11:30 AM, Mahmood Naderan <mahmood...@gmail.com>
wrote:

> it is interesting for me that I specified Verlet, but the log warns about
> group.
>
> mahmood@cluster:LPN$ grep -r cut-off .
> ./mdout.mdp:; cut-off scheme (group: using charge groups, Verlet: particle
> based cut-offs)
> ./mdout.mdp:; nblist cut-off
> ./mdout.mdp:; long-range cut-off for switched potentials
> ./mdout.mdp:; cut-off lengths
> ./mdout.mdp:; Extension of the potential lookup tables beyond the cut-off
> mahmood@cluster:LPN$ grep -r Verlet .
> ./mdout.mdp:; cut-off scheme (group: using charge groups, Verlet: particle
> based cut-offs)
> ./mdout.mdp:cutoff-scheme            = Verlet
> ./mdout.mdp:; Allowed energy drift due to the Verlet buffer in kJ/mol/ps
> per atom,
> ./mdout.mdp:coulomb-modifier         = Potential-shift-Verlet
> ./mdout.mdp:vdw-modifier             = Potential-shift-Verlet
>
>
>
>
> Regards,
> Mahmood
>
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