[gmx-users] mpi- gromacs
Mark.Abraham at anu.edu.au
Thu Oct 30 05:18:35 CET 2008
Chih-Ying Lin wrote:
> Here is my pdb file.
> #PBS -l nodes=2
> cat $PBS_NODEFILE
> echo Working directory is $PBS_O_WORKDIR
> cd $PBS_O_WORKDIR
> mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg
> 11 0
> Then, it showed
> Fatal error:
> No energy terms selected
g_energy is not MPI-aware - see
http://wiki.gromacs.org/index.php/Installation#Using_MPI - so don't
compile it, and don't attempt to run it in parallel. Most of the GROMACS
utility programs are intended to run from the command line rather than
on a compute cluster.
The above syntax is not how to use g_energy in an automated fashion. See
discussion of your options.
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