[gmx-developers] unidirectional neighbor list

[hessb at mpip-mainz.mpg.de]

Hi,

I assume that indeed the qmmm lists do what you want.
Also the normal lists can be modified easily to take all pairs into
account.
In src/mdlib/ns.c there are jcg0 and jcg1 which currently limit
the range of j particles. Also for large charge groups there is
a check in put_in_list.
But the question is what you want to do with those lists.
The Gromacs neighborlists are a bit complex structures.

Berk

> 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
>>
>
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