[gmx-users] Making Commands Non-Interactive

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 4 18:35:34 CEST 2009

ABEL Stephane 175950 wrote:
> Dear GMX Users,
> I ask this question in this mailing list since probably a user have already
> encountered this similar problem. I would like to  post-process my trajectory
> with the command trjconv (in mpi mode). For this I use the following shell
> command:

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

> 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. With the selection 0
> ("System")
> It works but since my simulations is very long (> 300ns) the command stops in
> the middle of the trajectory before to finish the process ( i suspect a time
> limit for using the interactive mode). So i would like to use a script to do
> the task. How to pass the choice 0 in the script (i.e. equivalent to the echo
> 0). I use a bash shell and the command qsub to launch a mpi job.
> I have tried to adapt the examples available in the GMX website with a text
> file as suggested by the author in GROMACS site with no success.

I routinely use a text file for scripted jobs.  Odd that yours isn't working. 
Is it just that the command still exits before finishing?  In any case, you can 
make an .ndx file with only an entry for [System].  When presented with one 
choice, trjconv has to choose it.


> Thank you again for your help
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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