[gmx-users] hydrophobic interactions

Sudip Das das.sudip37 at gmail.com
Fri Dec 28 12:17:46 CET 2018

Hi Andrew,

1) http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow
the 'g_sas' section)

2) You can use gmx_cluster module to do the cluster analysis. The central
frame of the most populated cluster will be the average structure.

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Fri, Dec 28, 2018 at 4:20 PM Andrew Bostick <andrew.bostick1 at gmail.com>

> Hi all,
> I did md simulation of protein-ligand complex using gromacs 5.1.3.
> 1) How to investigate hydrophobic interactions between protein and ligand
> during trajectory? Which tool is appropriate for this aim?
> 2) How to get an average structure from whole of trajectory?
> Best,
> Andrew
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