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    On 17/08/2011 9:13 PM, Kavyashree M wrote:
    <blockquote
cite="mid:CAPLGqjpJ=Da-9K_J73tA+Nf0hgdntQ=OQDQbAzLSdWWtb_b8Gg@mail.gmail.com"
      type="cite">Sir, <br>
      <br>
      I checked gmxdump -e ener.edr as suggested, I found that<br>
      there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5<br>
      when I calculated the average for these values using another<br>
      tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave <br>
      some different answer as mentioned before in both 4.5.3 and<br>
      4.5.4 versions. Sorry I sent the mail twice as I did not receive<br>
      Dr. Mark's reply form the forum.<br>
    </blockquote>
    <br>
    OK, that looks like a bug of some kind. Please file an issue at
    redmine.gromacs.org (the server is down at the moment) uploading
    your input and output files and I'll take a look at it. Thanks.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAPLGqjpJ=Da-9K_J73tA+Nf0hgdntQ=OQDQbAzLSdWWtb_b8Gg@mail.gmail.com"
      type="cite"><br>
      Thank you<br>
      With Regards<br>
      Kavya<br>
      <br>
      <br>
      <br>
      <div class="gmail_quote">On Wed, Aug 17, 2011 at 4:15 PM,
        Kavyashree M <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="margin:0 0 0
          .8ex;border-left:1px #ccc solid;padding-left:1ex;">
          Sorry Sir, <br>
          <br>
          I did not get that mail from the forum.<br>
          <br>
          Thank you<br>
          With Regards<br>
          Kavya
          <div>
            <div class="h5"><br>
              <br>
              <div class="gmail_quote">On Wed, Aug 17, 2011 at 12:11 PM,
                Tsjerk Wassenaar <span dir="ltr">&lt;<a
                    moz-do-not-send="true"
                    href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>&gt;</span>
                wrote:<br>
                <blockquote class="gmail_quote" style="margin:0 0 0
                  .8ex;border-left:1px #ccc solid;padding-left:1ex">This
                  mail was answered already... Please pay attention.<br>
                  <br>
                  <a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html"
                    target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html</a><br>
                  <br>
                  Tsjerk<br>
                  <div>
                    <div><br>
                      On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M &lt;<a
                        moz-do-not-send="true"
                        href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>&gt;
                      wrote:<br>
                      &gt; Dear users,<br>
                      &gt;<br>
                      &gt; While calculating the box dimensions during a
                      simulation<br>
                      &gt; of 20ns I got some strange values of the
                      averages -<br>
                      &gt;<br>
                      &gt; Command used:<br>
                      &gt; g_energy -f ener.edr -o box.xvg<br>
                      &gt;<br>
                      &gt; Output:<br>
                      &gt; Energy&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Average&nbsp;&nbsp;
                      Err.Est.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; RMSD&nbsp; Tot-Drift<br>
                      &gt;
-------------------------------------------------------------------------------<br>
                      &gt; Box-X&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.00665539&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
                      1.4&nbsp;&nbsp; 0.219101&nbsp;&nbsp; -4.28575&nbsp; (nm)<br>
                      &gt; Box-Y&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.00665606&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
                      1.4&nbsp;&nbsp; 0.219101&nbsp;&nbsp; -4.28574&nbsp; (nm)<br>
                      &gt; Box-Z&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.00470607&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
                      1&nbsp;&nbsp; 0.154928&nbsp;&nbsp; -3.03048&nbsp; (nm)<br>
                      &gt;<br>
                      &gt; While the actual dimensions are 7.2, 7.2 and
                      5.1 respectively. I use<br>
                      &gt; Gromacs-4.5.3, and 4.5.4 version also gave
                      the same error. But<br>
                      &gt; when the .xvg file is examined it does not
                      show much of the&nbsp; error<br>
                      &gt; indicated here. I also checked whether the is
                      any discontinuity in<br>
                      &gt; the .edr file using gmxcheck and there was
                      data from 0 to 20ns<br>
                      &gt; with no such discontinuity. I am attaching
                      the corresponding .xvg plot.<br>
                      &gt; I had a similar&nbsp; problem before, and I was
                      asked to check using<br>
                      &gt; the new version. Which I did ad there was no
                      difference. Meanwhile<br>
                      &gt; I calculated the average values using other
                      tools which gave 7.2, 7.2<br>
                      &gt; and 5.1 respectively. So What is the problem
                      here. Kindly clarify the<br>
                      &gt; confusion.<br>
                      &gt;<br>
                      &gt; Thanking you<br>
                      &gt; With Regards<br>
                      &gt; M. Kavyashree<br>
                      &gt;<br>
                    </div>
                  </div>
                  &gt; --<br>
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                  &gt;<br>
                  <br>
                  <br>
                  <br>
                  --<br>
                  Tsjerk A. Wassenaar, Ph.D.<br>
                  <br>
                  post-doctoral researcher<br>
                  Molecular Dynamics Group<br>
                  * Groningen Institute for Biomolecular Research and
                  Biotechnology<br>
                  * Zernike Institute for Advanced Materials<br>
                  University of Groningen<br>
                  The Netherlands<br>
                  <font color="#888888">--<br>
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