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    On 4/19/2011 2:57 PM, Sikandar Mashayak wrote:
    <blockquote
      cite="mid:BANLkTinODfmjXJ1TV8S9RMEqp-yb67R6Eg@mail.gmail.com"
      type="cite">so that means if I define a index group GRP and energy
      exclusion GRP GRP then all the non-boned interactions between
      atoms belonging to GRP group are excluded?<br>
    </blockquote>
    <br>
    What does manual 7.3.19 say?<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:BANLkTinODfmjXJ1TV8S9RMEqp-yb67R6Eg@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">On Mon, Apr 18, 2011 at 7:43 PM, Mark
        Abraham <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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 text="#000000" bgcolor="#ffffff">
            <div class="im"> On 4/18/2011 1:43 PM, Sikandar Mashayak
              wrote:
              <blockquote type="cite">Also, what about non-bonded
                interactions within the protein? Does exclusion group
                only exclude the non-bonded interactions between two
                different molecules and non-bonded interactions within
                the single molecule atoms are still computed?<br>
              </blockquote>
              <br>
            </div>
            The sets of atoms for energy groups and such exclusions are
            defined by the index groups, not molecules. See manual 7.3
            and wherever it talks about groups in an early chapter.
            <div class="im"><br>
              <br>
              <blockquote type="cite">
                <div class="gmail_quote">On Sun, Apr 17, 2011 at 10:38
                  PM, Sikandar Mashayak <span dir="ltr">&lt;<a
                      moz-do-not-send="true"
                      href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</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;"> Hi
                    <div><br>
                    </div>
                    <div>When we define energy group exclusions e.g.
                      like in manual&nbsp;<span style="font-size: 12px;
                        font-family: Helvetica;">energygrp excl =
                        Protein Protein SOL SOL&nbsp;</span></div>
                    <div><font face="Helvetica">and do md rerun, then
                        only non-bonded interactions between Protein and
                        SOL are computed. I am wondering what happens to
                        bonded interactions within the protein, do they
                        contribute to energies even though we have
                        excluded protein-protein interactions?</font></div>
                  </blockquote>
                </div>
              </blockquote>
              <br>
            </div>
            Bonded interactions are unaffected, as you will see if you
            try it.<br>
            <br>
            Mark<br>
            <br>
          </div>
          <br>
          --<br>
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        </blockquote>
      </div>
      <br>
    </blockquote>
    <br>
  
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