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.confli...@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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