[gmx-users] Print Neighbour list

[Paolo Conflitti]

Thank you for your answer.

Unfortunately, that is exactly what I am trying to do. However, what I 
need is more of a custom neighbour search for specific particle-water 
interactions (i.e. one atom against all the neighbour water molecules), 
than a completely new class. And I need to do it at runtime, since I 
will use this information as input for other operations.
However, I think I got the gist of it, thanks to your previous answer.

Again, thanks for everything.

Best,
Paolo

Il 28/01/2019 14:03, Mark Abraham ha scritto:
> Hi,
>
> gmx select does this kind of operation already, if what you want to do is
> not part of the simulation... It is implemented by its own simple but
> fairly efficient search. The neighbor search code is intended for
> consumption by the short-range kernels, and you do not want to get involved
> with that unless you have to!
>
> Mark
>
> On Mon, 28 Jan 2019 at 12:49 Paolo Conflitti <paolo.conflitti at gmail.com>
> wrote:
>
>> Thanks for your prompt reply.
>>
>> I wanted to print the neighbour list to better understand the way it is
>> processed.
>> I am currently trying to modify the Gromacs code in order to print only
>> the neighbour list of the water molecules around a certain atom. I got
>> inside the code and I found the algorithms that process this kind of
>> information, but I also wanted to see how the data are organized.
>> May I ask you if you know of a different way or variable (maybe a
>> commented line somewhere inside Gromacs) that will allow me to do
>> something similar?
>>
>> Best,
>> Paolo
>>
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