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    On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote:
    <blockquote
      cite="mid:AANLkTinD=yhAHBfdUTuFXRYezP=9RJ5dKJHpA-r07Zu0@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">Hi Chris,</div>
      <div class="gmail_quote"><br>
      </div>
      <div class="gmail_quote">On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof
        Mlynarczyk <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:mitomaster@gmail.com">mitomaster@gmail.com</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
          0.8ex; border-left: 1px solid rgb(204, 204, 204);
          padding-left: 1ex;">Hi,<br>
          <br>
          You need to use md integrator for -rerun to work.<br>
        </blockquote>
        <div><br>
        </div>
        <div>Aha, now it seems to work. Thanks!</div>
        <div><br>
        </div>
        <div>I am just sad that I did not find that information.
          According to <a moz-do-not-send="true"
            href="http://manual.gromacs.org/current/online/mdrun.html">http://manual.gromacs.org/current/online/mdrun.html</a> "With
          -rerun an input trajectory can be given for which forces and
          energies will be (re)calculated. Neighbor searching will be
          performed for every frame, unless nstlist is zero (see the
          .mdp file)."</div>
      </div>
    </blockquote>
    <br>
    Writing and documenting bulletproof software is tough work :-(<br>
    <br>
    I've fixed the code so that -rerun and EM or NM integrators flag a
    fatal error.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:AANLkTinD=yhAHBfdUTuFXRYezP=9RJ5dKJHpA-r07Zu0@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">
        <div> </div>
        <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
          0.8ex; border-left: 1px solid rgb(204, 204, 204);
          padding-left: 1ex;"><br>
          Good luck,<br>
          Chris<br>
          <br>
          <div class="gmail_quote">2010/11/6 Martin Kamp Jensen <span
              dir="ltr">&lt;<a moz-do-not-send="true"
                href="mailto:martin.kamp.jensen@gmail.com"
                target="_blank">martin.kamp.jensen@gmail.com</a>&gt;</span><br>
            <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
              0.8ex; border-left: 1px solid rgb(204, 204, 204);
              padding-left: 1ex;">
              <div>
                <div class="h5">Hello,
                  <div><br>
                  </div>
                  <div>Hopefully someone can help me understand how to
                    use the mdrun -rerun functionality, because
                    currently I am confused. I would like to be able to
                    look up potential energy values for a number of
                    conformations by calling mdrun -rerun once.</div>
                  <div><br>
                  </div>
                  <div>The idea to use mdrun -rerun is from advice given
                    to me by Mark Abraham on the gmx-developers list (<a
                      moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html"
                      target="_blank">http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html</a> and <a
                      moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html"
                      target="_blank">http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html</a>):</div>
                  <div><br>
                  </div>
                  <blockquote class="gmail_quote" style="margin: 0px 0px
                    0px 0.8ex; border-left: 1px solid rgb(204, 204,
                    204); padding-left: 1ex;">
                    You want GROMACS to find the energy of a potentially
                    infinite set of coordinates that appear magically,
                    and that is what mdrun -rerun does.</blockquote>
                  <blockquote class="gmail_quote" style="margin: 0px 0px
                    0px 0.8ex; border-left: 1px solid rgb(204, 204,
                    204); padding-left: 1ex;">
                    <br>
                  </blockquote>
                  <blockquote class="gmail_quote" style="margin: 0px 0px
                    0px 0.8ex; border-left: 1px solid rgb(204, 204,
                    204); padding-left: 1ex;">
                    The elegant way to do that is to write your series
                    of conformations to a pseudo-trajectory (in
                    whichever of GROMACS many trajectory formats is
                    convenient to you), and then invoke mdrun -rerun on
                    that trajectory with a suitable .tpr. Then you
                    either parse the .log file or the output .edr file
                    for the energies.</blockquote>
                  <div><br>
                  </div>
                  <div>I wanted to find out how this works so I have
                    been experimenting. I started out by looking at the
                    Peptide tutorial at <a moz-do-not-send="true"
                      href="http://manual.gromacs.org/current/online/speptide.html"
                      target="_blank">http://manual.gromacs.org/current/online/speptide.html</a>.
                    I used three different mdp files (integrator =
                    steep, nsteps = 0, 1, 2). This gave me three
                    conformations and their energy values. For testing
                    purposes I then wanted to get the energy values for
                    those three conformations using mdrun -rerun (and
                    since I already have the correct energy values it is
                    easy to verify the results).</div>
                  <div><br>
                    First, I created a trajectory by concatenating the
                    three conformations (gro files) into one gro file
                    (which is okay according to <a
                      moz-do-not-send="true"
                      href="http://manual.gromacs.org/current/online/gro.html"
                      target="_blank">http://manual.gromacs.org/current/online/gro.html</a>:
                    "gro files can be used as trajectory by simply
                    concatenating files"). I then used an mdp file with
                    integrator = steep and nsteps = 0 indicating that I
                    just want the energy value (listed in the output, in
                    the log file or by using g_energy). Now, by using
                    mdrun -s &lt;tpr file&gt; -rerun &lt;gro trajectory
                    file&gt; I only get the energy value for the first
                    conformation listed in the gro file used to create
                    the tpr file. The -rerun option does not seem to
                    have any effect at all.</div>
                  <div><br>
                  </div>
                  <div>I used the following commands three times to
                    create three different conformations (one
                    conf_mdrun.gro file for each time) with different
                    energy values. I am just setting nsteps to 0, 1, or
                    2 (integrator = steep) in em.mdp.</div>
                  <div><br>
                  </div>
                  <div>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx
                      -i top_pdb2gmx &lt;&lt; EOF</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      1</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      1</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      EOF</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      <br>
                    </blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      editconf -f conf_pdb2gmx -o conf_editconf -d 0.5</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      <br>
                    </blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      genbox -cp conf_editconf -cs -p top_pdb2gmx -o
                      conf_genbox</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      mv top_pdb2gmx.top top_genbox.top</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      <br>
                    </blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      grompp -f em -po em_grompp -c conf_genbox -p
                      top_genbox -o em_grompp</blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      <br>
                    </blockquote>
                    <blockquote class="gmail_quote" style="margin: 0px
                      0px 0px 0.8ex; border-left: 1px solid rgb(204,
                      204, 204); padding-left: 1ex;">
                      mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun
                      -g mdrun</blockquote>
                  </div>
                  <div><br>
                  </div>
                  <div>I was hoping the following would give me the
                    three energy values for the three conformations in
                    2+1+0.gro, which is the concatenation of the three
                    conf_mdrun.gro files from before. However, I just
                    get the energy value from the first conformation in
                    the file. Using the -rerun option does not make a
                    difference (I can put whatever after -rerun, even
                    files that do not exist, without any effect).</div>
                  <div><br>
                  </div>
                  <blockquote class="gmail_quote" style="margin: 0px 0px
                    0px 0.8ex; border-left: 1px solid rgb(204, 204,
                    204); padding-left: 1ex;">
                    grompp -f em -po em_grompp -c gro/2+1+0 -p
                    top_genbox -o em_grompp</blockquote>
                  <blockquote class="gmail_quote" style="margin: 0px 0px
                    0px 0.8ex; border-left: 1px solid rgb(204, 204,
                    204); padding-left: 1ex;">
                    <br>
                  </blockquote>
                  <blockquote class="gmail_quote" style="margin: 0px 0px
                    0px 0.8ex; border-left: 1px solid rgb(204, 204,
                    204); padding-left: 1ex;">
                    mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro</blockquote>
                  <div><br>
                  </div>
                  <div>Regards,</div>
                  <div>Martin.</div>
                  <br>
                </div>
              </div>
              --<br>
              gmx-users mailing list    <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"
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                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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              Can't post? Read <a moz-do-not-send="true"
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            </blockquote>
          </div>
          <br>
          <br>
          --<br>
          gmx-users mailing list    <a moz-do-not-send="true"
            href="mailto:gmx-users@gromacs.org">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"
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          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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        </blockquote>
      </div>
      <br>
      <div>Regards,<br>
      </div>
      <div>Martin.</div>
    </blockquote>
    <br>
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