[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.
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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