[gmx-users] Lie calculation

[David]

On Mon, 2005-03-07 at 12:09 -0800, Cesar Lopez wrote:
> Dear gromacs users:
> 
> I have a question about lie calculations, I know that
> lts of literature talk about lie calculations using
> cut-offs in coulomb and LJ energies, Is there any
> difference if I use Reaction field instead of cut-off,
> I mean, the error in calculations could be affected?.
> Another question, I know that it is necessary the
> calculation of Van der wals and coulomb energies, and
> I have seen that gromacs shows you the SR Coulomb, but
> what hapened with the Van der Wals??????, is part of
> the LJ???, sorry if the answer is obvius.
> 
van der waals = LJ, but do also check 14 interactions.

reaction field maybe slightly problematic as the dielectric constant in
protein is not the same as in water. difference for LIE may be small
though.
> Thank you very much
> 
> Cesar
> 
> 
> 	
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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