Hi, > 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...: #!/bin/bash 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 -- 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 _______________________________________________ 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
