[gmx-users] FW: Binding cavity analysis

Ullmann, Thomas thomas.ullmann at mpibpc.mpg.de
Sun Aug 12 00:33:59 CEST 2018

From: Wycliffe Omwansu [womwansu at gmail.com]
Sent: Saturday, August 11, 2018 7:29 AM
To: Ullmann, Thomas
Subject: Binding cavity analysis


I have a 2 microsecond trajectory of protein-ligand system. I want to calculate 3 things:
1. Time series of number of water molecules in binding cavity.
2. Volume evolution of in the binding cavity.
3. Water surface density evolution in the cavity.

How can I go about it using gromacs?

Thank you.


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