[gmx-users] Density of ligand molecules around a particular residue

Smith, Micholas D. smithmd at ornl.gov
Mon Jun 10 13:51:53 CEST 2019

gmx rdf should give you this. It will give you the radial distribution function of the ligand molecules about the specific residue.


Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
Sent: Friday, June 7, 2019 6:20:58 PM
To: gmx-users at gromacs.org
Subject: [EXTERNAL] [gmx-users] Density of ligand molecules around a particular residue

Hi all,

I want to calculate the density of ligand molecules around a particular residue. Is there a gromacs tool that can achieve this? I've explored gmx spatial, gmx densmap but have had no luck. Any guidance will be much appreciated.

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