I see in the .top file generated by pdb2gmx:<br>[ pairs ]<br>; ai aj funct c0 c1 c2 c3<br><br>The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do c2 and c3 parametrize electrostatic interactions? And what do they stand for respectively? Thanks!<br>
<br><br><div class="gmail_quote">2009/7/27 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;">
My problem is actually as follows:<br>
</blockquote>
<br></div>
Please describe in as full detail as reasonable the first time :-)<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have three groups of atoms: A, B and C. Now I want to keep full<br>
interaction between A-B and A-C, but only retain the repulsive part of VDW<br>
interaction between B-C. I'm using the OPLS force field. It seems to me that<br>
the parameters for OPLS in the .itp files are specified for each atom, so is<br>
there any way to treat the interaction pairwise?<br>
</blockquote>
<br></div>
Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That will be tedious if there are many such atoms. Read parts of chapter 5.<br>
<br>
Probably, no force field was parameterized to reproduce whatever it is you're trying to observe.<div><div></div><div class="h5"><br>
<br>
Mark<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>SUN Li<br>Department of Physics<br>Nanjing University, China<br>