<div>So there is no place to specify electrostatic interactions for pair interactions?</div>
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<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>
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<div class="im">Lee Soin wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">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<br>c2 and c3 parametrize electrostatic interactions? And what do they stand for<br>respectively? Thanks!<br></blockquote><br></div>No, they're two pairs of VDW parameters, one pair each for two possible states for a free-energy calculation. The tables in chapter 5 imply this, but it is not at all obvious to a newcomer.
<div class="im"><br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That<br>will be tedious if there are many such atoms. Read parts of chapter 5.<br>
</blockquote></blockquote><br></div>You should still do this.
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<div class="h5"><br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<div></div><br>-- <br>SUN Li<br>Department of Physics<br>Nanjing University, China<br>