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

Alexey Kaa akabedev at gmail.com
Thu Nov 22 18:49:38 CET 2018


You might want to take a look at *gmx mindist*, it is capable of counting
the number of contacts between the atoms of different groups during any
specific period of run. Also you can specify what distance is considered as
a contact initiation.


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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