[gmx-users] Writing out the neighbor list

[Mark Abraham]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>