I create a parallel job file with the following content #$ -N prep66 #$ -pe openmpi* 12 #$ -cwd #$ -q medium*
mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/editconf_mpi -f 66.pdb -o cnt.gro -bt cubic -box 5 5 5 -c mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/g_x2top_mpi -f cnt.gro -o cnt.top -ff opls -name CNT mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genbox_mpi -cp cnt.gro -cs spc216.gro -p cnt.top -o cntsol.gro mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genrestr_mpi -f cntsol.gro During the process of running it creates several temp.top files which have the correct output, however the final topology file I get has zero output. I would like to know if I am doing anything wrong. Regards, Michelle -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-file-tp5015266.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
