RE: [gmx-users] np command with GROMACS 4.0.4

2009-04-22 Thread kyungchan chae
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:gm

Re: [gmx-users] np command with GROMACS 4.0.4

2009-04-22 Thread Justin A. Lemkul
Halie Shah wrote: 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 -max

Re: [gmx-users] np command with GROMACS 4.0.4

2009-04-22 Thread David van der Spoel
Halie Shah wrote: 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 -maxwa