[gmx-users] Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?

[João Henriques]

Hi Hassan,

Yes, this is something that I usually do with MDAnalysis, but from
experience I've noticed that people are often reluctant to try it.
Therefore you could try playing with gmx_select. Something like this should
output the number of water oxygen atoms within 5 Å of residue 1 as a
function of time:
gmx_mpi select -f md.xtc -s md.tpr -os -select "name OW and within 0.5 of
resnr 1"

This is just an example, play around with the selection syntax and other
options to get the desired result.

Cheers,
J

On Thu, Nov 22, 2018 at 5:57 PM Hassan Aaryapour <hassan.gromacs at gmail.com>
wrote:

> Dear Gromacs Users
> I would like to calculate the presence of water molecules number as a
> function of time, around a ligand during binding to its pocket from a
> trj.xtc file.
> How can I do it by Gromacs or any other program?
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