[gmx-users] multiple outputs in mdrun with gromacs-4.0.3

[Mark Abraham]

vivek sharma wrote:
> Hi There,
> I have upgraded my Gromacs version from 3.3 to 4.0.3. I am using it with 
> mpi over 24 processor and 3 nodes (each node having 8 processor). I 
> fired an energy minimization run. while doing do, I found multiple 
> copies of output files (.edr, .gro, .trr) instead of single file.
> Following is the mdrun commnd line i used.
> "mpirun  -srun  
> /app/prod/bioinformatics/gromacs/4.0.3/intel/DP/bin/mdrun_d -s 
> 1XU9_A_em.tpr -o 1XU9_A_em.trr -c 1XU9_A_em.gro -g em.log -e em.edr  &"
> 
> Please suggest is there any correction in the command line to get the 
> output as I was getting with version-3.3

Probably you built an mpi version for 3.3 and a non-mpi version for 
4.0.3. Use the configure option to make a suitable suffix, like _mpi. 
Also, it's a good idea to install the latest GROMACS version, not one 
several months old.

Mark