<div dir="ltr">Hi David,<br><br>what is the main problem with RF? Why do you not recommend it? The paper <a href="http://www3.interscience.wiley.com/journal/79503038/abstract">Walser, Hünenberger, et.al.</a>, <a href="http://www.proteinscience.org/cgi/content/abstract/12/10/2161">Gargolla Hünenberger et.al.</a> <font size="-1"> </font>suggest that RF is OK for proteins and <a href="http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2002/106/i14/html/jp013855m.html">Nina and Simonson</a> say it is OK for RNA.<br>
<br>I'm thinking about using it since my 2D FFT won't be included in 4.0 and thus PME doesn't scale for large systems. The system is cellulose and lignin.<br><br>Thanks<br>Roland<br><br><div class="gmail_quote">
On Fri, Aug 29, 2008 at 2:26 PM, 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;">
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I also noted that there now is a recommendation against cut-offs (bad) but for PME (good) or reaction fields (almost as bad). This is of course a bit up to ones taste, but I would definitely argue against recommending RF.<div>
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-- <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>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>
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