[gmx-users] Making Commands Non-Interactive

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Sun Oct 4 18:22:44 CEST 2009

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: 

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. 

Thank you again for your help 

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