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

[Alexey Kaa]

Hi,

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.
http://manual.gromacs.org/programs/gmx-mindist.html

Best,
Aleksei




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?
> --
> 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.
>