[gmx-users] charged proteins

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Fri Mar 8 18:22:35 CET 2002

Hi Berk,

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?

Many tkanks,

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.
> Berk.

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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