Hi Gavin,
I had exactly the same problem a few days ago.
you have 2 options for parallel runs: domain decomposition (default) and
particle decomposition
you can either try to manipulate the parameters of your system such that
they fit domain decomposition or choose the easier way..that is using
pa
Gavin Melaugh wrote:
Hi all
I have a ran a simulation of 64 molecules in a cubic box with side 6 nm,
using nose-hoover thermostat, parinello-rahman pressure coupling, and
pme. Runnin the simulation in parallel is no problem (using 16 CPUs).
However when I want to run an almost identical molecu
Hi all
I have a ran a simulation of 64 molecules in a cubic box with side 6 nm,
using nose-hoover thermostat, parinello-rahman pressure coupling, and
pme. Runnin the simulation in parallel is no problem (using 16 CPUs).
However when I want to run an almost identical molecule using the exact
same c
hazizian wrote:
> hi
>
> I want to use mdrun, when i use It as one job it goes on.
> but when i use as parallel job
>
>> grompp -np 4 -f md300.mdp -c pr.pdb -p topol.top -o md300.tpr
>>
>
> then
>
>> mpirun -np 4 mdrungromacs_mpi -nice 0 -v -s md300.tpr -o md300.trr -c
>
hi
I want to use mdrun, when i use It as one job it goes on.
but when i use as parallel job
> grompp -np 4 -f md300.mdp -c pr.pdb -p topol.top -o md300.tpr
>
then
> mpirun -np 4 mdrungromacs_mpi -nice 0 -v -s md300.tpr -o md300.trr -c
md300.pdb -e md300.edr -g md300.log
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