<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    On 28/09/2011 9:11 AM, Martin Kamp Jensen wrote:
    <blockquote
cite="mid:CAFVEjokXcbqaJyCEcp3JK5DdRjOGscH_wx=GSV3mdQk2CfJcyA@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">On Tue, Sep 27, 2011 at 3:09 PM, Justin
        A. Lemkul <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="margin:0 0 0
          .8ex;border-left:1px #ccc solid;padding-left:1ex">
          <div><br>
            <br>
            Martin Kamp Jensen wrote:<br>
            <blockquote class="gmail_quote" style="margin:0 0 0
              .8ex;border-left:1px #ccc solid;padding-left:1ex">
              Hello,<br>
              <br>
              I need to combine several trajectories (.xtc) and energy
              file (.edr) pairs. In the end I need all the conformations
              of the trajectories and a specific energy value for each
              of them.<br>
              <br>
              To combine two trajectories, I use trjcat [1] like this:<br>
              <br>
              &nbsp; &nbsp;trjcat -f first.xtc second.xtc -o combined.xtc -cat<br>
              <br>
              <br>
              Since I just need the conformations (the coordinates) and
              I do not care about "step" and "time," I guess this is
              okay.<br>
              <br>
              To combine two energy files, it seems like I should use
              eneconv [2]. Unfortunately, there is not an argument like
              "-cat" for trjcat, which means that the tool will not
              include all energies from the input files in the output
              file ("In case of double time frames the one in the later
              file is used."). I should probably note that I do not need
              "Av. Energy" or "Sum Energy," I just need the energy
              frames in the energy files concatenated so that I can
              easily extract them and assign them to the correct
              conformations.<br>
              <br>
              Any ideas?<br>
              <br>
            </blockquote>
            <br>
          </div>
          Don't use the -cat option of trjcat. &nbsp;Normally you'll have
          duplicate time frames, for instance, in the final frame of
          "first.xtc" and the first frame of "second.xtc." &nbsp;If they are
          the same, you do not need to keep them. &nbsp;The -cat option, as I
          understand it, is basically for fudging different trajectories
          together for non-standard purposes. &nbsp;If you omit -cat then
          you'll have .edr and .xtc files that match.<br>
        </blockquote>
        <div><br>
        </div>
        <div>But my purposes are non-standard and I need all of the
          conformations of both (or more) input trajectories as well as
          the&nbsp;corresponding&nbsp;energy frames. I see that, per the
          description of "-cat," time and step information will be
          messed up, but that is not a problem.</div>
      </div>
    </blockquote>
    <br>
    So pre-process with -settime such that duplicate times cannot arise.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAFVEjokXcbqaJyCEcp3JK5DdRjOGscH_wx=GSV3mdQk2CfJcyA@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">
        <div><br>
        </div>
        <div>(I have created a program that reads conformations from a
          trajectory and assigns a specific energy value from a
          corresponding energy file to each of the conformations. I just
          had a special case where I was asked to work with several
          trajectories and energy files which were provided to me and it
          would be nice to just concatenate them and then not introduce
          special functionality in my program to handle it.)</div>
        <div>&nbsp;</div>
        <blockquote class="gmail_quote" style="margin:0 0 0
          .8ex;border-left:1px #ccc solid;padding-left:1ex">
          <br>
          -Justin
          <div><br>
            <br>
            <blockquote class="gmail_quote" style="margin:0 0 0
              .8ex;border-left:1px #ccc solid;padding-left:1ex">
              Regards,<br>
              Martin.<br>
              <br>
              [1] <a moz-do-not-send="true"
                href="http://manual.gromacs.org/online/trjcat.html"
                target="_blank">http://manual.gromacs.org/online/trjcat.html</a><br>
              [2] <a moz-do-not-send="true"
                href="http://manual.gromacs.org/online/eneconv.html"
                target="_blank">http://manual.gromacs.org/online/eneconv.html</a><br>
              <br>
            </blockquote>
            <br>
          </div>
          -- <br>
          ========================================<br>
          <br>
          Justin A. Lemkul<br>
          Ph.D. Candidate<br>
          ICTAS Doctoral Scholar<br>
          MILES-IGERT Trainee<br>
          Department of Biochemistry<br>
          Virginia Tech<br>
          Blacksburg, VA<br>
          jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
            target="_blank">vt.edu</a> | (540) 231-9080<br>
          <a moz-do-not-send="true"
            href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
            target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
          <br>
          ========================================<br>
          <font color="#888888">
            -- <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 www interface or send it to <a moz-do-not-send="true"
              href="mailto:gmx-users-request@gromacs.org"
              target="_blank">gmx-users-request@gromacs.org</a>.<br>
            Can't post? Read <a moz-do-not-send="true"
              href="http://www.gromacs.org/Support/Mailing_Lists"
              target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
          </font></blockquote>
      </div>
      <br>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
    </blockquote>
    <br>
  </body>
</html>