[gmx-users] neighbor list

Berk Hess gmx3 at hotmail.com
Thu Jan 15 12:15:02 CET 2004

> > I have a question about neighbor list construction. Is it correct that
> > the neighbor list is organized by charge groups? Ie an atom can be
> > within Rc but not in the list because its group is outside and the
> > other way around. Also, some solvents such as water are not in the
> > neighbor lists. Now, is there an option to build a neighbor list that
> > contains all atoms within Rc independent of their charge groups,
> > solvent type, etc?
>There is a 'grace distance' beyond the cut-off to prevent atoms that are
>within the cutoff to be 'forgotten' due to charge group being outside 
>(don't remember how large that is, though).
>Water is defenitely in the neighborlist, but probably has its own list
>entirely for performance reasons.
>I don't think the option you mention existsi.

There is no 'grace distance' in Gromacs.
A pair of atoms is put in the neighborlist if the centers of geometry of the 
charge groups
they belong to are inside the cut-off distance. Thus some atom pairs might 
not interact
while they are inside the cut-off distance, while other atom pairs might 
interact while
they are outside the cut-off distance.
These charge groups are important for simulations with cut-off 
electrostatics as they
reduce the cut-off noise significantly.
With shiftted electrostatics or PME charge groups are only important for 
performance reasons.

But why would you want atom-based neighborsearching?


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