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    On 4/05/2011 8:08 AM, Sikandar Mashayak wrote:
    <blockquote
      cite="mid:BANLkTikxD7Qoevd5d0kYfe3BXJMYwAuQZQ@mail.gmail.com"
      type="cite">yeah, it says PME cant be excluded using energy
      exclusion, so I am wondering about any other way to exclude it?<br>
    </blockquote>
    <br>
    There is none.<br>
    <br>
    One option is to run the simulation with PME for the improved
    sampling accuracy, and then to use mdrun -rerun&nbsp; with some other
    electrostatics method if you really think these forcefields'
    non-bonded interactions can be decompose groupwise and end up
    meaning something.<br>
    <br>
    There was an approach posted in the last month or two that does
    multiple reruns with PME to achieve the same effect.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:BANLkTikxD7Qoevd5d0kYfe3BXJMYwAuQZQ@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">On Tue, May 3, 2011 at 5:01 PM, Justin A.
        Lemkul <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;">
          <div>
            <div class="h5"><br>
              <br>
              Sikandar Mashayak 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>
                I want to compute only the non-bonded ( LJ + EL)
                interactions between Protein and Solvent and exclude
                non-bonded interactions between Protein Protein &amp;
                SOL SOL. <br>
                But energy exclusion group does not necessarily exclude
                the non-bonded electrostatic interactions while using
                PME option for coulombtype. <br>
                So I am just wondering if I were to compute
                electrostatic interactions between just Protein SOL with
                PME, how can I do that?<br>
                <br>
              </blockquote>
              <br>
            </div>
          </div>
          Hasn't this already been answered?<br>
          <br>
          <a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/2011-April/060594.html"
            target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-April/060594.html</a><br>
          <br>
          -Justin<br>
          <br>
          <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
            0.8ex; border-left: 1px solid rgb(204, 204, 204);
            padding-left: 1ex;">
            thanks<br>
            sikandar<br>
            <br>
            <br>
          </blockquote>
          <br>
          -- <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> | <a moz-do-not-send="true"
            href="tel:%28540%29%20231-9080" value="+15402319080"
            target="_blank">(540) 231-9080</a><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>
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