[gmx-users] charged proteins

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Thu Mar 7 19:45:35 CET 2002

Hi List, and thank you all very much for your attention.

 From all I've been reading here (including PME vs. Reaction-field
benchmarks) I conclude it:

Summarising. If I want to run a substrate/protein complex immersed in
water, no matter it is charged or not, I should use PME with counterions
(if need), right?
If not charged, just a long cut-off would give reasonable results, so a
faster option than with PME, ok?
Single precision is ok in both cases, isn't it?

On Thu, 7 Mar 2002, David van der Spoel wrote:

> On Thu, 7 Mar 2002, Alan Wilter Sousa da Silva wrote:
> >
> >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?
> For accuracy of the forces you want PME. Cut-offs introduce a lot of noise
> and artefacts in water orientation. For proteins in water, where
> electrostatic interactions are important, you need PME. Double precision
> is only necessray in special cases: accurate minimization before normal
> analysis, mdrun with polarizable shell particle.
> Actuall single precision PME runs have  very good energy conservation, you
> hardly need temperature coupling.
> 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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