[gmx-users] Running GROMACS in PBS

[Triguero, Luciano O]

Hello Everyone,
 
I have a small problem here and need your help. Let start telling that I had spend some time trying to solve the problem with the recommendations I found in the internet, however my problem persist.
 
I am running gromacs in a cluster and want to use one single machine with 4 nodes. When I submit mpimdrun directly to one of the node as (mpimdrun -np 4 -s filename.tpr -N 4) the program runs without problems. However, when I do the same command inside a script and sibmit it to the PBS system. I mean (qsub -q long run.job), mpimdrun doesn't work. Is there anybody in the list who has experienced a similar problem and know how to solve it. 
 
Thank in advance,
 
Luciano
 
 
 
Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938