[gmx-users] charged proteins
Alan Wilter Sousa da Silva
alan at biof.ufrj.br
Fri Mar 8 18:22:35 CET 2002
A system or 15000 or more atoms is not small, don't you think so? But
have you notice some PME artifacts with a system of 5000 or less atoms?
Where can read more about Reaction-field?
On Fri, 8 Mar 2002, Berk Hess wrote:
> I would say for any system with water, including a charged or
> uncharged protein and some or no counterions use at least a
> reaction field. Even in pure water a plain cut-off will give
> terrible artifacts.
> PME is more accurate than reaction-field, but not much,
> especially in a high dielectric solvent like water. You will
> have to choose for yourself if the gain in accuracy is worth
> the performance penalty. Also for very small systems PME might
> give periodicity artifacts.
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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