[gmx-users] REMD on more than one node

[Mark Abraham]

Hi,

You'll need to choose a replica setup that naturally fits on your available
hardware. Number of nodes * number of cores per node must equal number of
replicas * number of cores per replica. See also
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations

Mark

On Fri, May 13, 2016 at 4:41 AM YanhuaOuyang <15901283893 at 163.com> wrote:

> Hi,
> I am running a REMD with grimacs 5.0, I have 46 replica, 4 nodes, 16 cores
> per node. how can I use my compute resource and what’s the command of “gmx
> mdrun”?
> the command is below, I am not sure weather it is right
> mpirun -np 4 -npme gmx mdrun -s md_01.tpr  -multi 46 -replex 500 -reseed
> -1.
> mpirun -np 4 -npme gmx mdrun -s md_02.tpr  -multi 46 -replex 500 -reseed
> -1.
> mpirun -np 4 -npme gmx mdrun -s md_03.tpr  -multi 46 -replex 500 -reseed
> -1.
> …
> mpirun -np 4 -npme gmx mdrun -s md_46.tpr  -multi 46 -replex 500 -reseed
> -1.
>
>
> --
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