[gmx-developers] unidirectional neighbor list

[Maik Nijhuis]

Dear Gromacs developers,

Regarding the neighbor lists for the non-bonded interactions I have a 
question. I understood the neighbor lists are currently constructed 
based on bidirectional, pair-wise interactions: A particle pair only 
occurs once in the list, and the forces for both particles are updated 
when the non-bonded kernel computes the interaction.

I am interested if Gromacs has an option for generating unidirectional 
neighbor lists, which contains all neighbors for each atom, instead of 
all neighbor pairs. All atoms then occur as i atom in the list, and due 
to periodic boundary conditions they may occur multiple times. All 
particle pairs thus occur twice: once as (i,j), once as (j, i).

Does anybody know if it is currently possible to generate the neighbor 
lists this way?

Maik Nijhuis
-- 
mnijhuis at virtualproteins.com || http://www.cs.vu.nl/~maik