[gmx-developers] unidirectional neighbor list

[Gerrit Groenhof]

You can check how the qmmm nblists are consructed. For each i charge 
group of the qm subsystem all j particles within the long range cut-off 
are collected. I think this is what you want, right?

Gerrit

Maik Nijhuis wrote:
> 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
>