[gmx-users] Lie calculation
spoel at xray.bmc.uu.se
Mon Mar 7 21:25:34 CET 2005
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
> Thank you very much
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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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