Hi there,<br><br>Try giving the complete address of the command you want to run, just like this:<br><br>/usr/bin/grompp -f *.mdp -c *.gro -p *.top -o *.tpr -np 4<br><br>mpirun -np 4 /usr/bin/mdrun_mpi.lam -s *.tpr -x *.xtc -c *.gro -g *.log -e *.edr -v
<br><br>The address depends on your installation. In my case is /usr/bin/.<br><br>I hope it helps,<br>Diego.<br><br><br><div><span class="gmail_quote">2007/8/6, Anupam Nath Jha <<a href="mailto:anupam@mbu.iisc.ernet.in">
anupam@mbu.iisc.ernet.in</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear all<br><br>i am new in gromacs. i have installed
gromacs-3.3.3 in our cluster(mpi is<br>already there) with parallel version (using the following command):<br><br><br>make clean<br>./configure --enable-mpi --disable-nice --program-suffix="_mpi"<br>make mdrun<br>
make install-mdrun<br><br>it went fine.<br><br>but when i ran the command -<br>qsub pbs_submit<br><br>it's the pbs_submit file:<br><br>#This is a PBS script for Parallel Jobs<br>#!/bin/bash -f<br>#PBS -l nodes=2:ppn=2
<br>#PBS -o /home/anupam/MD/lyd<br>#PBS -e /home/anupam/MD/lyd<br>#PBS -q default<br><br>cd /home/anupam/MD/lyd<br>mpirun grompp -f em.mdp -p topol.top -c solvated.gro -np 4 -o em.tpr<br>mpirun mdrun_mpi -v -deffnm -np 4 em
<br><br>but it's not doing anything,except writing this:<br><br>totalnum=3 numhosts=2<br>there are not enough hosts on which to start all processes<br>totalnum=3 numhosts=2<br>there are not enough hosts on which to start all processes
<br><br><br><br>can you help me out?<br><br>thanks in adavnce<br>anupam<br><br><br><br>--<br>Science is facts; just as houses are made of stone, so is science is made of<br>facts; but a pile of stones is not a house, and a collection of facts is not
<br>necessarily sciece.<br><br>Anupam Nath Jha<br>Ph. D. Student<br>Saraswathi Vishveshwara Lab<br>Molecular Biophysics Unit<br>IISc,Bangalore-560012<br>Karnataka<br>Ph. no.-22932611<br><br><br><br>--<br>This message has been scanned for viruses and
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