Hi,<br />I have exactly the same problem as is described below. I am using version 4.5.4 with the Plumed metadynamics plugin.<br /><br />I was wondering if there was any update on dealing with the bug?<br /><br />Many thanks,<br />Jen<br /><br />Today's Topics:<br />
<div class="replyBody">
<blockquote class="email_quote" style="border-left: 2px solid #267fdb; margin: 0pt 0pt 0pt 1.8ex; padding-left: 1ex;"><br /> 1. Re: Replica Exchange MD using Gromacs (Mark Abraham)<br /> 2. Re: FW: protein split over boundary (ravi sharma)<br /> 3. Re: FW: protein split over boundary (Justin A. Lemkul)<br /><br /><br />----------------------------------------------------------------------<br /><br />Message: 1<br />Date: Fri, 01 Apr 2011 22:30:56 +1100<br />From: Mark Abraham <<a class="parsedEmail" href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br />Subject: Re: [gmx-users] Replica Exchange MD using Gromacs<br />To: Discussion list for GROMACS users <<a class="parsedEmail" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br />Message-ID: <<a class="parsedEmail" href="mailto:4D95B770.1070805@anu.edu.au" target="_blank">4D95B770.1070805@anu.edu.au</a>><br />Content-Type: text/plain; charset="iso-8859-1"<br /><br />On 1/04/2011 6:52 PM, bsmith wrote:<br />> On 01/04/2011, at 6:29 PM, Mark Abraham wrote:<br />><br />>> On 1/04/2011 6:03 PM, Ruchi Gupta wrote:<br />>>> Dear gmx-users,<br />>>><br />>>> I am facing some problems while running replica exchange MD using <br />>>> Gromacs.<br />>>><br />>>> Few seconds after the job submission it ends with the following <br />>>> error message:<br />>>><br />>>> "<br />>>> Initializing Replica Exchange<br />>>><br />>>> Repl There are 6 replicas:<br />>>> Multi-checking the number of atoms ... OK<br />>>> Multi-checking the integrator ... OK<br />>>> Multi-checking init_step+nsteps ...<br />>>> init_step+nsteps is not equal for all subsystems<br />>>> subsystem 0: 0<br />>>><br />>>> subsystem 1: 50000<br />>>> subsystem 2: 0<br />>>> subsystem 3: 50000<br />>>> subsystem 4: 0<br />>>> subsystem 5: 50000<br />>>><br />>>> -------------------------------------------------------<br />>>> Program mdrun, VERSION 4.5.4<br />>>> Source code file: main.c, line: 249<br />>>><br />>>><br />>>> Fatal error:<br />>>> The 6 subsystems are not compatible<br />>>><br />>>> For more information and tips for troubleshooting, please check the <br />>>> GROMACS<br />>>> website at<a class="parsedLink" href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br />>>><br />>>> -------------------------------------------------------<br />>>><br />>>> "<br />>>><br />>>> I am using a "single .gro file" and "6 different md.mdp" files (at 6 <br />>>> different temperatures) for generating "6 .tpr files", respectively. <br />>>> But the simulation doesn't work.<br />>>><br />>>><br />>>> I have compared the ".tpr files" using "gmxdump" and "gmxcheck" <br />>>> Gromacs commands and they seem fine with respect to nsteps and <br />>>> init_step information.<br />>><br />>> So, to be clear, gmxcheck says that for no pair of .tprs does <br />>> 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 class="parsedEmail" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <br />>> <<a class="parsedLink" href="mailto:gmx-users@gromacs.org" target="_blank">mailto:gmx-users@gromacs.org</a>><br />>> <a class="parsedLink" 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 <br />>> <a class="parsedLink" href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br />>> Please don't post (un)subscribe requests to the list. Use the www <br />>> interface or send it to <a class="parsedEmail" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br />>> Can't post? Read <a class="parsedLink" href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br />><br />> 1) Comparison of the .tpr files using gmxdump reveals no differences <br />> but for the temperatures and the velocities in each i.e. init_step and <br />> nsteps have the same values (0 and 50000, respectively) in all files.<br />><br />> 2) We have tried running mdrun without checkpointing (-cpt -1) and <br />> with checkpointing with no change in the outcome.<br /><br />That sounds like a bug. Please create a new Redmine issue here <br /><a class="parsedLink" href="http://redmine.gromacs.org" target="_blank">http://redmine.gromacs.org</a> and attach your .tpr and .mdp files - <br />preferably in a compressed archive file. You should get the option to <br />assign it to me - please do.<br /><br />Mark<br />-------------- next part --------------<br />An HTML attachment was scrubbed...<br />URL: <a class="parsedLink" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110401/471a7c08/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110401/471a7c08/attachment-0001.html</a><br /><br /><br /></blockquote>
</div>