[gmx-users] charged proteins

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 7 22:02:54 CET 2002

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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