You don't need to use -np 4 option to do preprocessing on version 4.0.4. Just do preprocessing without it and use it when you start your simulation like followings:
grompp mpirun -np 4 mdrun (if you use MPI for parallel running) kyungchan From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Halie Shah Sent: Wednesday, April 22, 2009 4:01 PM To: gmx-users@gromacs.org Subject: [gmx-users] np command with GROMACS 4.0.4 Hi! I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command: grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -maxwarn 10 and it gave me the response that -np is an invalid command. How do I get grompp to rec. that I want to use 4 processors? Because my job script where I have specified 4 nodes, will not work unless I have np 4 included in my grompp. I did see that it works with GROMACS 3.3.3...but is there a way to do it with 4.0.4? Thanks so much! Halie Shah University of Houston, TX U.S. Briggs Lab
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