[gmx-users] PME User
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jul 12 17:49:22 CEST 2008
Sang-Min Park wrote:
> Dear all,
> I read in www.gromacs.org/gromacs/revisions/ in the report of
> David van der Spoel
> "Added support for a combination of PME and User determined coulomb
> potentials. The user has to take care that the combination of Coulomb and
> standard PME makes sense" ( 8 Feb. 2005)
> I don't understand what that means.
> As I know the Ewald Sum consist of the reciprocal and direct space term
> which are derivated for the f(x)=1/r function.
> In this sense I don't know what gromacs would do when I would specify
> PME-User with a potential that is different from f(x).
> 1. Can someone explain me what gromacs is doing when one sets PME-User ?
Let's say you want to replace the Coulomb potential Fc(r) by your own
Fuser(r). Then you have to subtract the Long Range part of the coulomb
potential Fc(r,LR) from your F(r) in the short range potential to get
the correct sum. Note that this also dependent on the cut-off, so if you
decide to change the cut-off you need a new lookup table for the
> 2. Furthermore I would like to know if the user defined potential tables are
> also used to calculate the long range interactions.
> Thank you for your time
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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