<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    On 04/16/2012 12:07 PM, Erik Marklund wrote:
    <blockquote
      cite="mid:ECF400BE-5993-462E-BC10-9581A3009E9D@xray.bmc.uu.se"
      type="cite">
      <meta http-equiv="Content-Type" content="text/html;
        charset=ISO-8859-1">
      <br>
      <div>
        <div>16 apr 2012 kl. 11.32 skrev Erik Marklund:</div>
        <br class="Apple-interchange-newline">
        <blockquote type="cite">
          <div>Hi,<br>
            <br>
            I have a few trajectories from simulations of solvated
            proteins and DNA that causes problems when I pass them
            through trjconv. Here's the command line:<br>
            <br>
            trjconv &nbsp;-f run.xtc -s run.tpr -o tst.xtc -pbc mol<br>
            <br>
            Choosing group "Protein" for output, I get heaps of
            inconsistent shits:<br>
            <br>
            "...<br>
            There were 1 inconsistent shifts. Check your topology00 time
            4000.000 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br>
            There were 1 inconsistent shifts. Check your topology<br>
            ..."<br>
            <br>
            These trajectories were saved frequently, some every 10 ps.
            If I use -dt 1000 the errors disappear, probably because I
            skip certain problematic frames. No problems were reported
            in the logfiles from the simulations and this problem
            appears in braches release-4-6 and release-4-5-patches, and
            the official 4.5.5 release. The simulations were all done
            with release-4-5-patches.<br>
            <br>
            To me this looks like a bug.<br>
          </div>
        </blockquote>
        <div><br>
        </div>
        <div><br>
        </div>
        I gess my qustion is: should I file a redmine?</div>
    </blockquote>
    Does you xtc file contain a non-contiguous subset of the system?<br>
    In that case your issue is probably already filed.<br>
    <br>
    Cheers,<br>
    <br>
    Berk<br>
    <blockquote
      cite="mid:ECF400BE-5993-462E-BC10-9581A3009E9D@xray.bmc.uu.se"
      type="cite">
      <div><br>
        <blockquote type="cite">
          <div><br>
            -----------------------------------------------<br>
            Erik Marklund, PhD<br>
            Dept. of Cell and Molecular Biology, Uppsala University.<br>
            Husargatan 3, Box 596, &nbsp;&nbsp;&nbsp;75124 Uppsala, Sweden<br>
            phone: &nbsp;&nbsp;&nbsp;+46 18 471 6688 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;fax: +46 18 511 755<br>
            <a moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br>
            <a class="moz-txt-link-freetext" href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a><br>
            <br>
            --<br>
            gmx-developers mailing list<br>
            <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
            <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-developers">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
            Please don't post (un)subscribe requests to the list. Use
            the<br>
            www interface or send it to
            <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
          </div>
        </blockquote>
      </div>
      <br>
      <div>
        <span class="Apple-style-span" style="border-collapse: separate;
          color: rgb(0, 0, 0); font-family: Helvetica; font-style:
          normal; font-variant: normal; font-weight: normal;
          letter-spacing: normal; line-height: normal; orphans: 2;
          text-align: -webkit-auto; text-indent: 0px; text-transform:
          none; white-space: normal; widows: 2; word-spacing: 0px;
          -webkit-border-horizontal-spacing: 0px;
          -webkit-border-vertical-spacing: 0px;
          -webkit-text-decorations-in-effect: none;
          -webkit-text-size-adjust: auto; -webkit-text-stroke-width:
          0px; font-size: medium; "><span class="Apple-style-span"
            style="border-collapse: separate; color: rgb(0, 0, 0);
            font-family: Helvetica; font-style: normal; font-variant:
            normal; font-weight: normal; letter-spacing: normal;
            line-height: normal; orphans: 2; text-align: -webkit-auto;
            text-indent: 0px; text-transform: none; white-space: normal;
            widows: 2; word-spacing: 0px;
            -webkit-border-horizontal-spacing: 0px;
            -webkit-border-vertical-spacing: 0px;
            -webkit-text-decorations-in-effect: none;
            -webkit-text-size-adjust: auto; -webkit-text-stroke-width:
            0px; font-size: medium; ">
            <div style="word-wrap: break-word; -webkit-nbsp-mode: space;
              -webkit-line-break: after-white-space; "><span
                class="Apple-style-span" style="border-collapse:
                separate; color: rgb(0, 0, 0); font-family: Helvetica;
                font-style: normal; font-variant: normal; font-weight:
                normal; letter-spacing: normal; line-height: normal;
                orphans: 2; text-indent: 0px; text-transform: none;
                white-space: normal; widows: 2; word-spacing: 0px;
                -webkit-border-horizontal-spacing: 0px;
                -webkit-border-vertical-spacing: 0px;
                -webkit-text-decorations-in-effect: none;
                -webkit-text-size-adjust: auto;
                -webkit-text-stroke-width: 0px; font-size: medium; ">
                <div style="word-wrap: break-word; -webkit-nbsp-mode:
                  space; -webkit-line-break: after-white-space; ">
                  <div>-----------------------------------------------</div>
                  <div>Erik Marklund, PhD</div>
                  <div>Dept. of Cell and Molecular Biology, Uppsala
                    University.</div>
                  <div>Husargatan 3, Box 596, &nbsp; &nbsp;75124 Uppsala, Sweden</div>
                  <div>phone: &nbsp; &nbsp;+46 18 471 6688 &nbsp; &nbsp; &nbsp; &nbsp;fax: +46 18 511
                    755</div>
                  <div><a moz-do-not-send="true"
                      href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div>
                  <div><a moz-do-not-send="true"
                      href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div>
                </div>
              </span></div>
          </span></span>
      </div>
      <br>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
    </blockquote>
    <br>
  </body>
</html>