Thanks Erik, <br>In case I run my simulations on 4 nodes, please let me know what do I have to add to the command to start "MPI"? I have used the commands:<br><i>grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top<br>
mdrun -s NVT_50ns -o NVT_50ns -c NVT_50ns -x NVT_50ns -e NVT_50ns -g NVT_50ns -v</i><br>however, the speed was still the same.<br>Best regards,<br><br>Cuong<br><br><div class="gmail_quote">2012/3/15 Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">If you are to run on a single node, then there's no need for mpi nowadays. mdrun uses all cores it can find anyway. If you need to split your calculation over many machines, however, you will need mpi.<div>
<br></div><div>Best,</div><div><br></div><div>Erik<br><div><br><div><div>15 mar 2012 kl. 04.50 skrev cuong nguyen:</div><br><blockquote type="cite"><div><div class="h5"><div>Dear Gromacs users,</div>
<div> </div>
<div>I prepare to run my simulations on the supercomputer on single node with 64 CPUs. Although I have seen on Gromacs Mannual suggesting to use MPI to parellel, I still haven't understood how to use this application and which commands I have to use. Please help me to deal with this?</div>
<div> </div>
<div>Many thanks and regards,</div>
<div> </div>
<div>Cuong</div>
<div> </div><br></div></div><div class="im">
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<div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: <a href="tel:%2B46%2018%20471%206688" value="+46184716688" target="_blank">+46 18 471 6688</a> fax: <a href="tel:%2B46%2018%20511%20755" value="+4618511755" target="_blank">+46 18 511 755</a></div>
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