[gmx-users] neighbor list

Eric Jakobsson jake at ncsa.uiuc.edu
Sun Jan 18 00:52:01 CET 2004

Our group is of the view that if you don't use PME, you should definitely 
use neutral group-based groups.  If you don't, you see distinct artifacts 
in the radial distribution functions at the cut-off distance.  That 
evidence convinced us.


At 05:17 AM 1/15/2004 -0800, you wrote:

>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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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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