On 12/21/09 5:32 PM, Yanmei Song wrote:
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.
Read the manual please.
On Mon, Dec 21, 2009 at 12:48 AM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:
On 12/21/09 8:03 AM, Yanmei Song wrote:
Dear Users:
Anyone can explain why the density of the water models increase with
increase the cutoff length. I tried a couple water models in
reaction-field, PME simulations.The cutoff length ranged from 0.9 to
1.5. They all show the same trend. Then there must be some reasons.
Anyone can tell me why?
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
Van der Waals interactions. I guess you have not turned on the
dispersion correction. If you do the effect should be far less.
--
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.
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> sp...@gromacs.org
<mailto:sp...@gromacs.org> http://folding.bmc.uu.se
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--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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