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

João Henriques joao.m.a.henriques at gmail.com
Thu Nov 22 18:17:06 CET 2018

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.


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

> 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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