[gmx-users] neighbor list
mic0404 at yahoo.com
Thu Jan 15 14:18:01 CET 2004
Berk Hess wrote:
> These charge groups are important for simulations with cut-off
> electrostatics as they
> reduce the cut-off noise significantly.
its not so much about the noise, the point with charge
groups is that you end up with electrostatic interactions
between only dipoles (which go with 1/r^3) and no
more monopole-monopole interactions ( 1/r ).
Thus the electrost. interaction is (seeemingly) shorter ranged
(though still not converging for r-cut -> infinity) giving
results that are less system-size dependent; whether they
are correct is a different question ...
but there still is the question: is in Gromacs only the generation
the neighbour-list group-based or also the calculation of
the electrostatic interactions (which is nor necessarily the same
> With shiftted electrostatics or PME charge groups are only important for
> performance reasons.
I am not sure whether group-based cut-off in combination
with PME is a good idea, and If you don't use PME there are
still reasons to avoud group-based cut-offs, see, e.g.,
Biophys J, September 2000, p. 1537-1553, Vol. 79, No. 3;
there is also a more rigorous investigation of the subject
by Hummer G., the exact reference eludes me for know ...
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