[gmx-users] Writing out the neighbor list

[Alan Manning]

Ah OK. I'll probably implement a neighbor list after the fact from the 
trajectory data itself. Thanks.

On 15-03-09 03:17 PM, Mark Abraham wrote:
> Hi,
>
> Not really. gmx mdrun -debug n for sufficiently large n (3?) will print out
> the IDs of the i and j clusters that are in the cluster-pair list for its
> duration, but of course that's buffered and does not correspond directly to
> anything that leads to physics. To get a list of particles that interact at
> a given time step, you'd have to hack a C kernel that also dumped the atom
> indices of pairs that were actually within the cutoff; very doable for the
> single-domain case, but not already done for you.
>
> Mark
>
> On Mon, Mar 9, 2015 at 9:48 PM, Alan Manning <mannin2 at physics.ubc.ca> wrote:
>
>> Hi
>>
>> Is it possible to have Gromacs write out the neighbor lists as well as the
>> trajectories? Thanks.
>>
>> Regards,
>> Alan Manning
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