[gmx-users] charged proteins
Alan Wilter Sousa da Silva
alan at biof.ufrj.br
Thu Mar 7 18:54:56 CET 2002
I believe there would have a polarization with charged protein specially
using periodic boundary conditions (I'd like hear more here). However,
and here goes my question, should not 'cut-off' avoid this problem? And
with no charged protein, should I use PME? If so, for better results I'd
have to use 'double-precison', wouldn't I?
On Thu, 7 Mar 2002, David van der Spoel wrote:
> On Thu, 7 Mar 2002, jozef hritz wrote:
> > Dear Jocelyne,
> >my oppinion is that for reliable simulation You have add to system
> >counterions to charged aminoacids. Whole system should be electroneutral.
> Indeed, and use PME.
> Groeten, David.
> Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576, 75123 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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Alan Wilter S. da Silva
Laboratório de Física Biológica
Instituto de Biofísica Carlos Chagas Filho
Universidade do Brasil/UFRJ
Rio de Janeiro, Brasil
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