[gmx-users] Fwd: Help regarding Gromac installation with MPI

sachin hegde itssach75 at gmail.com
Thu Jan 26 19:13:00 CET 2006


I am trying to run the Gromacs benchmark with ammasso 1100 according
to this doc :http://www.ammasso.com/tt_gromacs.pdf
and am stuck at the last step, that is at the mpirun command. I was able to

grompp -f cutoff.mdp
-c conf.gro -p topol.top -po mdout.mdp -shuffle -sort -np 4

The next step is to run mpirun
mpirun -np 4 ~/gromacs/g321/x86_64-unknown-linux-gnu/bin/mdrun -s topol.tpr
-o traj.trr -c confout.gro -e ener.edr -g md.lot -np 4

This step doesnt seem to work as it says that the file or command was
not found. I am pointing them to the correct paths, but dont know why
its not recognizing it.

Tried linking the the mdrun binary (~/gromacs/g321/.../mdrun) to the
current directory (i.e., where your topol.tpr is), and then use
'mpirun -np 4
/mdrun -s topol.tpr', as suggested by Anton, but still doesnt work,
gives me the error
Line 0: /usr/bin/env...unable to find file or directory..
Thankx in advance,

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