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    On 6/04/2012 3:53 PM, bipin singh wrote:
    <blockquote
cite="mid:CAKb2Z-Hk6mf0zZgsGH9TceOejmt6TXFjPwkEQHgBSHvUxkS-Gg@mail.gmail.com"
      type="cite">Yes you are right, that we need to do multiple MD runs
      before making any conclusion based on single trajectory. But I
      have not found any single research paper which discuss about
      conclusions drawn based on ensemble of trajectories. If you have
      any such research article then please send me the link.<br>
    </blockquote>
    <br>
    Doubtless there are others, but Tsjerk's
    <a class="moz-txt-link-freetext" href="http://dx.doi.org/10.1021/jp068580v">http://dx.doi.org/10.1021/jp068580v</a> is a good start.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAKb2Z-Hk6mf0zZgsGH9TceOejmt6TXFjPwkEQHgBSHvUxkS-Gg@mail.gmail.com"
      type="cite">
      <br>
      <div class="gmail_quote">On Thu, Apr 5, 2012 at 23:50, Peter C.
        Lai <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:pcl@uab.edu">pcl@uab.edu</a>&gt;</span> wrote:<br>
        <blockquote class="gmail_quote" style="margin:0 0 0
          .8ex;border-left:1px #ccc solid;padding-left:1ex">
          Well you're really supposed to conduct multiple runs anyway.<br>
          Remember, a single MD run over a period of time only samples 1
          possible<br>
          trajectory out of the ensemble of possible trajectories...<br>
          <br>
          On 2012-04-05 11:38:20PM +0530, bipin singh wrote:<br>
          &gt; Thanks for the reply.<br>
          &gt; * *I read the link. So, how one can predict something
          reliable using these<br>
          <div class="im">&gt; results(based on 50ns in my case) which
            changes on different machines?<br>
            &gt; which depends more on the environment of the computer
            architecture and<br>
            &gt; other variables of mdrun rather than system
            (Protein/DNA/RNA) itself for a<br>
            &gt; short simulation, where we don't have enough resources
            to run infinitely<br>
            &gt; long simulation.<br>
            &gt; And also how to believe the statement made by several
            research papers based<br>
            &gt; on unconverged simulations.<br>
            &gt;<br>
            &gt; On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul &lt;<a
              moz-do-not-send="true" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;
            wrote:<br>
            &gt;<br>
            &gt; &gt;<br>
            &gt; &gt;<br>
            &gt; &gt; bipin singh wrote:<br>
            &gt; &gt;<br>
            &gt; &gt;&gt; Hi all,<br>
            &gt; &gt;&gt;<br>
            &gt; &gt;&gt; I am really surprised to see different results
            from two identical md<br>
            &gt; &gt;&gt; simulation. I have used identical tpr files
            for the mdrun (for 50ns) and<br>
            &gt; &gt;&gt; after the completion of the md job I found
            that the results from the<br>
            &gt; &gt;&gt; identical runs is totally different.<br>
            &gt; &gt;&gt;<br>
            &gt; &gt;&gt; To further confirm this, I have converted both
            the input tpr to mdp using<br>
            &gt; &gt;&gt; gmxdump and diff the two files and found that
            the mdp is identical.<br>
            &gt; &gt;&gt;<br>
            &gt; &gt;&gt; Please let me know what can be the reason of
            this behaviour. I know that<br>
            &gt; &gt;&gt; it is unexpected and even I can't believe how
            can it be possible.<br>
            &gt; &gt;&gt;<br>
            &gt; &gt;&gt;<br>
            &gt; &gt; It is not unexpected at all. &nbsp;Please consult:<br>
            &gt; &gt;<br>
          </div>
          &gt; &gt; <a moz-do-not-send="true"
href="http://www.gromacs.org/**Documentation/Terminology/**Reproducibility"
            target="_blank">http://www.gromacs.org/**Documentation/Terminology/**Reproducibility</a>&lt;<a
            moz-do-not-send="true"
            href="http://www.gromacs.org/Documentation/Terminology/Reproducibility"
            target="_blank">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a>&gt;<br>
          &gt; &gt;<br>
          &gt; &gt; -Justin<br>
          &gt; &gt;<br>
          &gt; &gt; --<br>
          &gt; &gt; ==============================**==========<br>
          <div class="im">&gt; &gt;<br>
            &gt; &gt; Justin A. Lemkul<br>
            &gt; &gt; Ph.D. Candidate<br>
            &gt; &gt; ICTAS Doctoral Scholar<br>
            &gt; &gt; MILES-IGERT Trainee<br>
            &gt; &gt; Department of Biochemistry<br>
            &gt; &gt; Virginia Tech<br>
            &gt; &gt; Blacksburg, VA<br>
            &gt; &gt; jalemkul[at]<a moz-do-not-send="true"
              href="http://vt.edu" target="_blank">vt.edu</a> | (540)
            231-9080<br>
          </div>
          &gt; &gt; <a moz-do-not-send="true"
            href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>**<a
            moz-do-not-send="true"
            href="http://vt.edu/Pages/Personal/justin" target="_blank">vt.edu/Pages/Personal/justin</a>&lt;<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>&gt;<br>
          &gt; &gt;<br>
          &gt; &gt; ==============================**==========<br>
          <div class="im">&gt; &gt; --<br>
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          &gt;<br>
          &gt; --<br>
          &gt; -----------------------<br>
          &gt; *Regards,*<br>
          &gt; Bipin Singh<br>
          <div class="im"><br>
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            --<br>
          </div>
==================================================================<br>
          <span class="HOEnZb"><font color="#888888">Peter C. Lai &nbsp; &nbsp; &nbsp;
              &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;| University of Alabama-Birmingham<br>
              Programmer/Analyst &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;| KAUL 752A<br>
              Genetics, Div. of Research &nbsp; &nbsp; &nbsp;| 705 South 20th Street<br>
              <a moz-do-not-send="true" href="mailto:pcl@uab.edu">pcl@uab.edu</a>
              &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | Birmingham AL 35294-4461<br>
              (205) 690-0808 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;|<br>
==================================================================<br>
            </font></span>
          <div class="HOEnZb">
            <div class="h5"><br>
              --<br>
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            </div>
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        </blockquote>
      </div>
      <br>
      <br clear="all">
      <br>
      -- <br>
      <span style="color:rgb(51,51,255)">-----------------------</span><br
        style="color:rgb(51,51,255)">
      <i><span style="color:rgb(51,51,255)">Thanks and Regards,</span></i><br
        style="color:rgb(51,51,255)">
      <span style="color:rgb(51,51,255);font-family:garamond,serif">Bipin
        Singh</span><br>
      <br>
      <br>
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      <br>
    </blockquote>
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