Hi there, Try giving the complete address of the command you want to run, just like this:
/usr/bin/grompp -f *.mdp -c *.gro -p *.top -o *.tpr -np 4 mpirun -np 4 /usr/bin/mdrun_mpi.lam -s *.tpr -x *.xtc -c *.gro -g *.log -e *.edr -v The address depends on your installation. In my case is /usr/bin/. I hope it helps, Diego. 2007/8/6, Anupam Nath Jha <[EMAIL PROTECTED]>: > > Dear all > > i am new in gromacs. i have installed gromacs-3.3.3 in our cluster(mpi is > already there) with parallel version (using the following command): > > > make clean > ./configure --enable-mpi --disable-nice --program-suffix="_mpi" > make mdrun > make install-mdrun > > it went fine. > > but when i ran the command - > qsub pbs_submit > > it's the pbs_submit file: > > #This is a PBS script for Parallel Jobs > #!/bin/bash -f > #PBS -l nodes=2:ppn=2 > #PBS -o /home/anupam/MD/lyd > #PBS -e /home/anupam/MD/lyd > #PBS -q default > > cd /home/anupam/MD/lyd > mpirun grompp -f em.mdp -p topol.top -c solvated.gro -np 4 -o em.tpr > mpirun mdrun_mpi -v -deffnm -np 4 em > > but it's not doing anything,except writing this: > > totalnum=3 numhosts=2 > there are not enough hosts on which to start all processes > totalnum=3 numhosts=2 > there are not enough hosts on which to start all processes > > > > can you help me out? > > thanks in adavnce > anupam > > > > -- > Science is facts; just as houses are made of stone, so is science is made > of > facts; but a pile of stones is not a house, and a collection of facts is > not > necessarily sciece. > > Anupam Nath Jha > Ph. D. Student > Saraswathi Vishveshwara Lab > Molecular Biophysics Unit > IISc,Bangalore-560012 > Karnataka > Ph. no.-22932611 > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
