[gmx-users] charged proteins

[Alan Wilter Sousa da Silva]

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