My problem is actually as follows:<br>I have three groups of atoms: A, B and C. Now I want to keep full interaction between A-B and A-C, but only retain the repulsive part of VDW interaction between B-C. I'm using the OPLS force field. It seems to me that the parameters for OPLS in the .itp files are specified for each atom, so is there any way to treat the interaction pairwise?<br>
<br><br><div class="gmail_quote">2009/7/26 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Lee Soin wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello!<br>
I've read from the manual that the mdp option energygrp_excl can exclude<br>
pairs of energy groups for non-bonded interactions. But now I would like to<br>
remove all other non-bonded interactions but retain the repulsive part of<br>
the VDW interaction for a pair of energy group. Is there a way to do so?<br>
</blockquote>
<br></div>
Use grompp -pp to get a fully preprocessed .top file, and edit that to zero all the charges and dispersive LJ parameters.<br>
<br>
Mark<br>
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</blockquote></div><br><br clear="all"><br>-- <br>SUN Li<br>Department of Physics<br>Nanjing University, China<br>