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On 4/18/2011 1:43 PM, Sikandar Mashayak wrote:
<blockquote
cite="mid:BANLkTik5WPpOs31SMGrmd=YXGWwkeENXgA@mail.gmail.com"
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>
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.<br>
<br>
<blockquote
cite="mid:BANLkTik5WPpOs31SMGrmd=YXGWwkeENXgA@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Sun, Apr 17, 2011 at 10:38 PM,
Sikandar Mashayak <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:symashayak@gmail.com">symashayak@gmail.com</a>></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 <span style="font-size: 12px; font-family:
Helvetica;">energygrp excl = Protein Protein SOL SOL </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>
Bonded interactions are unaffected, as you will see if you try it.<br>
<br>
Mark<br>
<br>
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