[gmx-users] mpi- gromacs

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> 
> Here is my pdb file.
> #!/bin/bash
> #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 
  http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive for 
discussion of your options.

Mark