[gmx-users] neighbor list

[Anton Feenstra]

Maria Nemirovskaya wrote:

> Hi,
> 
> 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 cutoff.
(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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|