[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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