[gmx-users] Analyze neighbors of a residue within a cutoff distance during simulation

Smith, Micholas D. smithmd at ornl.gov
Tue Sep 1 14:19:57 CEST 2015

Hi Tushar Ranjan Moharana,

g_select (or gmx select if using gromacs version >5) will let you make an index file for each frame then you just have to loop through the index file and report the distances. You would make a selection like (you'll need to double check to make sure this is an accurate selection)

group "Methanol" and within 0.4 of group "Protein"

This will generate an index file that has the all of the methanol molecules within 0.nm4 of the protein at each time step as different groups. You should be able to write a script from there that will give you the average distance.


Micholas Dean Smith, PhD.
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 Tushar Ranjan Moharana <tusharranjanmoharana at gmail.com>
Sent: Tuesday, September 01, 2015 5:15 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Analyze neighbors of a residue within a cutoff distance    during simulation

Hi Everyone,
I have simulated a protein in 40 % methanol. Now I want to analyze the
average distance between any amino acid and all the methanol molecule which
comes to close to (less than 0.4 nm) that amino acid during the simulation.
I tried many GROMACS analysis tool for this but I couldn't succeed. Can
anybody kindly suggest me which analysis tool will be useful for me.

Thanks a lot in advance.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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