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.
-Justin
Thank you again for your help
------------------------------------------------------------------------
_______________________________________________ gmx-users mailing list
[email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to [email protected]. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
