[gmx-users] -np switch

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 15 01:23:59 CEST 2009

Payman Pirzadeh wrote:
> Hello,
> When we use ‘mdrun’ or ‘grompp’ with the switch ‘-np’ we specify the 
> number of nodes according to the manual. Does it mean if the nodes have 
> 2 processors, then the simulation will be run on 4 CPUs or in –np we 
> should specify 4 instead of 2?

Tell GROMACS the number of MPI processes you want. If you have two 
dual-core, dual-processor nodes, that might be 8 processes, etc. Your 
MPI setup may need to be configured to tell it how to distribute the 

grompp -np is not needed or available in GROMACS 4.x


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