<div>Hi, Mark:</div>
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<div>I made the index file and call two methanes as methane1 and methane2 , then I set energygrp_excl = methane1 methane2, but when I run grompp, it said methane1 is not an energy group. What do you understand this problem? Thanks. -Xianghong Qi<br>
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<div class="gmail_quote">On Wed, Nov 19, 2008 at 2:17 AM, xianghong qi <span dir="ltr"><<a href="mailto:xianghong001@gmail.com">xianghong001@gmail.com</a>></span> wrote:<br>
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<div>Yes, Mark. I now understand. I use united atom model. In my system, protein includes only methane pair. I still need those parameter to control protein/solvent, solvent/solvent interaction. Thanks so much for your great help. I will do it now. </div>
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<div>Best, -Xianghong Qi<br><br></div>
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<div class="gmail_quote">On Wed, Nov 19, 2008 at 1:48 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div>xianghong qi wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks, Mark. That means I can set energygrp_excl = Protein Protein, then I can get rid of those parameter which are related to electrostatics, Vdw( like rcoulomb, vdw-type, rvdw, rvdw-switch, etc). Am I right?<br>
</blockquote><br></div>No. Section 7.3.19 indicates how this should be done. I think you want<br><br>energygrp_excl = Methane1 Methane2<br><br>so you will need to use make_ndx suitably to create these groups.<br><br>If "Protein" includes only your pair of methanes, then<br>
<br>energygrp_excl = Protein Protein<br><br>will have the same effect, only because there are no intramolecular nonbonded interactions in methane. It's thus not a generalizable solution...
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