[gmx-users] Making Commands Non-Interactive

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Oct 4 19:27:12 CEST 2009


> Is trjconv parallelizable?  This is nowhere in the documentation, but if it
> is, that would be very interesting...

Well, the most interesting part in that regard is probably the I/O.
But that's the hardest bit to parallelize.

>> How to pass the choice 0 in the script

Just as you would on the command line...:


echo 0 | /usr/pbs/bin/mpiexec
/scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr
-f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc
mol -ur compact

Didn't you try?

There may be a problem, as the script is probably executed in the home
directory. So you need to add a line changing to the right directory;
just as you have done in interactive mode.

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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