[gmx-users] Lie calculation

David 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
> Cesar
> __________________________________ 
> Celebrate Yahoo!'s 10th Birthday! 
> Yahoo! Netrospective: 100 Moments of the Web 
> http://birthday.yahoo.com/netrospective/
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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

More information about the gromacs.org_gmx-users mailing list