Thanks for all the helpful response. But do I have to use dispersion correction when I use PME? I don't quite understand what dispersion correction do. Sometime I found using dispersion correction make my results worse for a large molecule system. <br>
<br><div class="gmail_quote">On Mon, Dec 21, 2009 at 12:48 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5">On 12/21/09 8:03 AM, Yanmei Song wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Users:<br>
<br>
Anyone can explain why the density of the water models increase with<br>
increase the cutoff length. I tried a couple water models in<br>
reaction-field, PME simulations.The cutoff length ranged from 0.9 to<br>
1.5. They all show the same trend. Then there must be some reasons.<br>
Anyone can tell me why?<br>
<br>
--<br>
Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
<br>
</blockquote></div></div>
Van der Waals interactions. I guess you have not turned on the dispersion correction. If you do the effect should be far less.<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>