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    On 1/04/2011 6:52 PM, bsmith wrote:
    <blockquote
      cite="mid:D03A28BF-C526-4A69-8CC0-FA0931B47AF1@wehi.edu.au"
      type="cite">
      <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 &nbsp;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"> &nbsp;&nbsp;subsystem 0: 0<br>
              </blockquote>
              <blockquote type="cite"><br>
              </blockquote>
              <blockquote type="cite"> &nbsp;&nbsp;subsystem 1: 50000<br>
              </blockquote>
              <blockquote type="cite"> &nbsp;&nbsp;subsystem 2: 0<br>
              </blockquote>
              <blockquote type="cite"> &nbsp;&nbsp;subsystem 3: 50000<br>
              </blockquote>
              <blockquote type="cite"> &nbsp;&nbsp;subsystem 4: 0<br>
              </blockquote>
              <blockquote type="cite"> &nbsp;&nbsp;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
                  moz-do-not-send="true"
                  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 &nbsp;&nbsp;&nbsp;<a moz-do-not-send="true"
                href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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                href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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            </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>
    </blockquote>
    <br>
    That sounds like a bug. Please create a new Redmine issue here
    <a class="moz-txt-link-freetext" href="http://redmine.gromacs.org">http://redmine.gromacs.org</a> and attach your .tpr and .mdp files -
    preferably in a compressed archive file. You should get the option
    to assign it to me - please do.<br>
    <br>
    Mark<br>
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