[gmx-users] neighbor list

[Anton Feenstra]

Berk Hess wrote:

>> Hi,
>>
>> Anton Feenstra wrote:
>>
>> 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.
[...]
> There is no 'grace distance' in Gromacs.

IIRC, there used to be a 'diffusion' radius, what I referred to as a
'grace distance' used for neigborlist generation, but not for force
calculation. That is, the neighborlist would always include too many
charge-group pairs, but the interactions were always calculated up
to the real cut-off distance, for charge groups. I see now my first
statement mentions atoms, which is not correct. If this has
disappeared, I wonder what is the reason for that, since it seems to
me a reasonable scheme to allow for diffusion of chargegroups inbetween
neighborlist updates...?


-- 
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)                               |
|_____________|_______________________________________________________|