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    On 1/02/2011 7:50 AM, Sai Pooja wrote:
    <blockquote
      cite="mid:AANLkTimjwhUf9KXdRWZCu3TEsRDOqqb6EqCqr-zAjfLD@mail.gmail.com"
      type="cite">
      <div>I think I have figured out the reason. It is because I am
        carrying out replica exchange (manual)&nbsp;after every mdrun. If the
        exchange occurs, I exchange the checkpoint files, extend the
        simulation by 500 steps and continue. The new simulation starts
        from exchanged cptfile. It seems that whenever the exchange
        occurs, the earlier log,traj files are not appended. They are
        instead overwritten. the obv solution is to save and index these
        files with the relevant replicas&nbsp;everytime an exchange occurs. </div>
    </blockquote>
    <br>
    This would have been good to know earlier. If replica-exchange leads
    to the ensemble of the .tpr not matching the ensemble of the .cpt,
    then IIRC 4.5.3 mdrun will refuse to start from the .cpt, which
    means the subsequent mdrun will start from the .tpr only. Certainly
    a non-appending mdrun prints a warning (or error, I forget which)
    message to the log file, but perhaps the use of -append
    (erroneously) doesn't do that. Please have a look and see if that is
    the issue. There is an environment variable that can be set to tell
    mdrun that you (think you) know what you are doing mismatching .tpr
    and .cpt.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:AANLkTimjwhUf9KXdRWZCu3TEsRDOqqb6EqCqr-zAjfLD@mail.gmail.com"
      type="cite">
      <div>However, i have a more general question. Since mdrun still
        runs with the exchanged checkpoint files and starts from the
        point where the previous run ended, can I be assured that an
        exchange has been affected - since tpr files correspond to the
        "replica-box" and cpi to the most recent exchanged replicas?</div>
      <div>&nbsp;</div>
      <div>Pooja<br>
        <br>
      </div>
      <div class="gmail_quote">On Mon, Jan 31, 2011 at 2:33 PM, Sai
        Pooja <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="padding-left: 1ex;
          margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
          204, 204);">
          <div><br>
            I manually index checkpoint files after every mdrun. What
            troubles me is the randomness with which -append
            fails/works.</div>
          <div>&nbsp;</div>
          <div>For eg, I have a simulation which runs from 3ns, 1ps in 1
            mdrun. Now oddly enough, the logfile starts from 1184ps(in
            the end, I do remember the one starting from 0 but that was
            overwritten it seems) and the rest is appended uptil the
            3000ps step. Why would append work from 1184ps to 3000ps but
            not for the previous ones?Could it have anything to do with
            the network/cluster? If that is the case is it safer to
            create a new file everytime and then concatenate them after
            say every 100ps?</div>
          <div>&nbsp;</div>
          <font color="#888888">
            <div>Pooja<br>
            </div>
          </font>
          <div class="gmail_quote">
            <div>
              <div class="h5">On Sat, Jan 29, 2011 at 6:52 PM, Mark
                Abraham <span dir="ltr">&lt;<a moz-do-not-send="true"
                    href="mailto:Mark.Abraham@anu.edu.au"
                    target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span>
                wrote:<br>
              </div>
            </div>
            <blockquote class="gmail_quote" style="padding-left: 1ex;
              margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
              204, 204);">
              <div>
                <div class="h5">
                  <div bgcolor="#ffffff" text="#000000">
                    <div>On 30/01/2011 10:39 AM, Sai Pooja wrote:
                      <blockquote type="cite">I would be happy to supply
                        more information.. if someone could please look
                        into this.. otherwise I will have to switch to
                        storing every file and then just concatenating
                        them which seems like a rather roundabout way of
                        doing it.<br>
                      </blockquote>
                      <br>
                    </div>
                    As I suggested a few emails ago, are you sure that
                    -cpi file exists? If your numerical suffixes are
                    indexing restarts, then unless you've done some
                    manual copying that you haven't told us about, it
                    won't. Your filename scheme seems a bit contorted -
                    like you're trying to do the work that GROMACS 4.5.x
                    will just do for you if you let it.<br>
                    <br>
                    Otherwise, you'll have to do some detective work
                    with gmxcheck on the -cpi to see what might be the
                    issue.<br>
                    <br>
                    In your case, an initial<br>
                    <br>
                    mdrun -deffnm rex_3<br>
                    <br>
                    (perhaps save some copies while you're
                    experimenting) and subsequently<br>
                    <br>
                    tpbconv -extend &lt;blah&gt; -f rex_3 -o rex_3<br>
                    mdrun -deffnm rex_3 -append<br>
                    <br>
                    will work and be much simpler than whatever you're
                    trying to do with filenames :-)<br>
                    <font color="#888888"><br>
                      Mark</font>
                    <div>
                      <div><br>
                        <br>
                        <blockquote type="cite"><br>
                          <div class="gmail_quote">On Fri, Jan 28, 2011
                            at 4:37 PM, Sai Pooja <span dir="ltr">&lt;<a
                                moz-do-not-send="true"
                                href="mailto:saipooja@gmail.com"
                                target="_blank">saipooja@gmail.com</a>&gt;</span>
                            wrote:<br>
                            <blockquote class="gmail_quote"
                              style="padding-left: 1ex; margin: 0px 0px
                              0px 0.8ex; border-left: 1px solid rgb(204,
                              204, 204);">
                              <div>This is the command:</div>
                              <div>&nbsp;</div>
                              <div>nbs submit -command
                                "(/usr/local/gromacs/4.5.1/bin/mdrun_mpi
                                -s rex_3.tpr -e rex_3 -c after_rex_3
                                -cpi restart3 -cpo restart3 -ap<br>
                                pend -g rexlog3 -x rextraj3);" -nproc 1
                                -name "GENHAM-DIHEDRAL-3" -mail start
                                end</div>
                              <div>&nbsp;</div>
                              <font color="#888888">
                                <div>Pooja<br>
                                  <br>
                                </div>
                              </font>
                              <div>
                                <div>
                                  <div class="gmail_quote">On Fri, Jan
                                    28, 2011 at 4:20 PM, Mark Abraham <span
                                      dir="ltr">&lt;<a
                                        moz-do-not-send="true"
                                        href="mailto:Mark.Abraham@anu.edu.au"
                                        target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span>
                                    wrote:<br>
                                    <blockquote class="gmail_quote"
                                      style="padding-left: 1ex; margin:
                                      0px 0px 0px 0.8ex; border-left:
                                      1px solid rgb(204, 204, 204);">
                                      <div>
                                        <div>On 29/01/2011 3:56 AM, Sai
                                          Pooja wrote:<br>
                                          <blockquote
                                            class="gmail_quote"
                                            style="padding-left: 1ex;
                                            margin: 0px 0px 0px 0.8ex;
                                            border-left: 1px solid
                                            rgb(204, 204, 204);">Hi,<br>
                                            I am using tpbconv and mdrun
                                            to extend a simulation. I
                                            use it with the append
                                            option but the files still
                                            get overwritten or erased.
                                            Can someone help me in this
                                            regard?<br>
                                            Pooja<br>
                                            Commands (in python)<br>
                                            cmd = '(%s/tpbconv -extend
                                            %f -s rex_%d.tpr -o
                                            rex_%d.tpr)'
                                            %(GROMPATH,dtstep,i,i)<br>
                                            &nbsp; &nbsp; &nbsp;os.system(cmd)<br>
                                            &nbsp; &nbsp; &nbsp;time.sleep(1)<br>
                                            &nbsp; &nbsp; &nbsp;cmd &nbsp;= 'nbs submit
                                            -command "'<br>
                                            &nbsp; &nbsp; &nbsp;cmd += '(%s/mdrun_mpi
                                            -noh -noversion -s
                                            rex_%d.tpr -e rex_%d -c
                                            after_rex_%d -cpi restart%d
                                            -cpo restart%d -append -g
                                            rexlog%d -x rextraj%d
                                            &gt;/dev/null); '
                                            %(GROMPATH,i,i,i,i,i,i,i)<br>
                                            &nbsp; &nbsp; &nbsp;cmd += '" '<br>
                                            &nbsp; &nbsp; &nbsp;cmd += '-nproc 1 '<br>
                                            &nbsp; &nbsp; &nbsp;cmd += '-name
                                            "GENHAM-DIHEDRAL-%d" '%(i)<br>
                                            &nbsp; &nbsp; &nbsp;cmd += '-mail start end
                                            '<br>
                                            &nbsp; &nbsp; &nbsp;cmd += '-elapsed_limit
                                            16h &gt;&gt; rexid'<br>
                                            &nbsp; &nbsp; &nbsp;os.system(cmd)<br>
                                          </blockquote>
                                          <br>
                                        </div>
                                      </div>
                                      More useful for diagnostic and
                                      record-preservation purposes is to
                                      construct the cmd string and print
                                      it to stdout (or something).<br>
                                      <br>
                                      At the moment it is far from clear
                                      that your -cpi file exists for the
                                      new run.<br>
                                      <br>
                                      Mark<br>
                                      <font color="#888888">-- <br>
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                                      </font></blockquote>
                                  </div>
                                  <br>
                                  <br clear="all">
                                  <br>
                                </div>
                              </div>
                              <div>
                                <div>-- <br>
                                  Quaerendo Invenietis-Seek and you
                                  shall discover.<br>
                                </div>
                              </div>
                            </blockquote>
                          </div>
                          <br>
                          <br clear="all">
                          <br>
                          -- <br>
                          Quaerendo Invenietis-Seek and you shall
                          discover.<br>
                        </blockquote>
                        <br>
                      </div>
                    </div>
                  </div>
                  <br>
                </div>
              </div>
              --
              <div class="im"><br>
                gmx-users mailing list &nbsp; &nbsp;<a moz-do-not-send="true"
                  href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
                <a moz-do-not-send="true"
                  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 moz-do-not-send="true"
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<br>
                www interface or send it to <a moz-do-not-send="true"
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                  target="_blank">gmx-users-request@gromacs.org</a>.<br>
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              </div>
            </blockquote>
          </div>
          <div>
            <div class="h5"><br>
              <br clear="all">
              <br>
              -- <br>
              Quaerendo Invenietis-Seek and you shall discover.<br>
            </div>
          </div>
        </blockquote>
      </div>
      <br>
      <br clear="all">
      <br>
      -- <br>
      Quaerendo Invenietis-Seek and you shall discover.<br>
    </blockquote>
    <br>
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