[gmx-users] charged proteins

[David van der Spoel]

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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