[gmx-users] RF, was: Re: Gromacs 4.0 beta

[Roland Schulz]

Hi David,

what is the main problem with RF? Why do you not recommend it? The
paper Walser,
Hünenberger, et.al.<http://www3.interscience.wiley.com/journal/79503038/abstract>,
Gargolla Hünenberger
et.al.<http://www.proteinscience.org/cgi/content/abstract/12/10/2161>
  suggest that RF is OK for proteins and Nina and
Simonson<http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2002/106/i14/html/jp013855m.html>say
it is OK for RNA.

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.

Thanks
Roland

On Fri, Aug 29, 2008 at 2:26 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

>
>
> 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.
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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