[gmx-users] Writing out the neighbor list

[Mark Abraham]

Hi,

Sure, you can do that e.g. with gmx select or your own code. I would think
gmx mdrun -rerun calling a C kernel with <10-line printf hack would be the
fastest to develop and then to run.

Mark

On Tue, Mar 10, 2015 at 1:06 AM, Alan Manning <mannin2 at physics.ubc.ca>
wrote:

> 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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