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>
<br><div class="gmail_quote">On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak <span dir="ltr"><<a href="mailto:symashayak@gmail.com">symashayak@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;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>
<div><font face="Helvetica"><br></font></div><div><font face="Helvetica">thanks</font></div><div><font face="Helvetica">sikandar</font></div>
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