[gmx-users] Print Neighbour list

[Mark Abraham]

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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