<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>On 01/04/2011, at 6:29 PM, Mark Abraham wrote:</div><div><div><br class="Apple-interchange-newline"><blockquote type="cite"><div>On 1/04/2011 6:03 PM, Ruchi Gupta wrote:<br><blockquote type="cite">Dear gmx-users,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am facing some problems while running replica exchange MD using Gromacs.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Few seconds after the job submission it ends with the following error message:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">"<br></blockquote><blockquote type="cite">Initializing Replica Exchange<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Repl There are 6 replicas:<br></blockquote><blockquote type="cite">Multi-checking the number of atoms ... OK<br></blockquote><blockquote type="cite">Multi-checking the integrator ... OK<br></blockquote><blockquote type="cite">Multi-checking init_step+nsteps ...<br></blockquote><blockquote type="cite">init_step+nsteps is not equal for all subsystems<br></blockquote><blockquote type="cite"> subsystem 0: 0<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> subsystem 1: 50000<br></blockquote><blockquote type="cite"> subsystem 2: 0<br></blockquote><blockquote type="cite"> subsystem 3: 50000<br></blockquote><blockquote type="cite"> subsystem 4: 0<br></blockquote><blockquote type="cite"> subsystem 5: 50000<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><blockquote type="cite">Program mdrun, VERSION 4.5.4<br></blockquote><blockquote type="cite">Source code file: main.c, line: 249<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Fatal error:<br></blockquote><blockquote type="cite">The 6 subsystems are not compatible<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">For more information and tips for troubleshooting, please check the GROMACS<br></blockquote><blockquote type="cite">website at<a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am using a "single .gro file" and "6 different md.mdp" files (at 6 different temperatures) for generating "6 .tpr files", respectively. But the simulation doesn't work.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have compared the ".tpr files" using "gmxdump" and "gmxcheck" Gromacs commands and they seem fine with respect to nsteps and init_step information.<br></blockquote><br>So, to be clear, gmxcheck says that for no pair of .tprs does init_step or nsteps differ...<br><br>What is your mdrun command line? Are you using checkpoint files?<br><br>Mark<br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br></div>1) Comparison of the .tpr files using gmxdump reveals no differences but for the temperatures and the velocities in each i.e. init_step and nsteps have the same values (0 and 50000, respectively) in all files.<div><br></div><div>2) We have tried running mdrun without checkpointing (-cpt -1) and with checkpointing with no change in the outcome.</div><div><br></div><div>Regards</div><div><br></div><div>Brian</div><div><br></div><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Dr Brian J Smith</font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">The Walter & Eliza Hall Institute of Medical Research</font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">1G Royal Parade, Parkville, Victoria 3052, Australia</font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Ph: +61 (0)3 9345 2687 Fax: +61 (0)3 9345 2686</font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.wehi.edu.au/brian_smith">http://www.wehi.edu.au/brian_smith</a></p><br class="Apple-interchange-newline"></span></div></span><br class="Apple-interchange-newline"> </div><br><BR>
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