<div style="font-size: 16px; font-family: 'times new roman'"><div><br /></div><div>On 01/01/10, <b class="name">Asmaa Elsheshiny </b><pyaaea@leeds.ac.uk> wrote:</div><blockquote cite="mid: <415005A809955F49AEEAF87A0566BD5C011BDDF429FA@HERMES8.ds.leeds.ac.uk" class="iwcQuote" style="padding-left: 13px; margin-left: 0px; border-left: #00f 1px solid" type="cite">Dear gromacs users,<br />I tried to make MD simulation using mdrun in the super computer by using the following script:<br />#!/bin/sh<br />#$ -cwd –V<br />#$ -l h_rt=1:00:00<br />#$ -pe mx* 4<br />export DO_PARALLEL=”/usr/local/sge6.0/mpi/myrinet/sge_mpirun”<br />export gromacs=/apps/gromacs/64/3.3.1-ffamber20080701/bin<br />$ DO_PARALLEL $gromacs/mdrun “ -s md.tpr \<br /> -o md.trr -x md.xtc –c md.gro –e ener.edr”<br />This script appears to work fine, but i stopped suddenly after a short period giving missing output. That is why the structure file .gro is missing. I have tested it locally before submitting it as a job in the supercomputer; I found that it works fine. So, what is the problem with this script?</blockquote><div ><br/></div><div>There are various problems. The space after the dollar sign and before DO_PARALLEL breaks its function. That mdrun needs to be compiled with MPI enabled, and the recommended installation guides on the website all recommend using configure options to append _mpi to MPI-enabled mdrun, so that you have a better chance of constructing command lines that do what you intend. Further, GROMACS 3.3.1 is years old, and unless you need scientific continuity with previous work, you will get much better simulation performance from 4.0.7.</div><div ><br/></div><div>Mark</div><div> </div><blockquote cite="mid: <415005A809955F49AEEAF87A0566BD5C011BDDF429FA@HERMES8.ds.leeds.ac.uk" class="iwcQuote" style="padding-left: 13px; margin-left: 0px; border-left: #00f 1px solid" type="cite"><div class="mimepart text plain"><br />Kind regards,<br />Asmaa<br /><br />-- <br />gmx-users mailing list gmx-users@gromacs.org<br /><a _zipIdx="577" href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />Please search the archive at <a _zipIdx="577" href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br />Please don't post (un)subscribe requests to the list. Use the <br />www interface or send it to gmx-users-request@gromacs.org.<br />Can't post? Read <a _zipIdx="577" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br /></div></blockquote></div>