[gmx-users] Cluster analysis on molecules

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Sat Mar 3 14:38:33 CET 2018

Hi all,

I want to calculate the number of clusters of my glycine molecules during the course of my simulation. I have read that gmx clustsize is the correct command to use. I read on one of the previous threads that I will have to create a separate tpr file for the molecules of interest. I also stripped the original trajectory to make a new one with glycine molecules only. I run the command below:

gmx clustsize -f glycine.gro -s glycine.tpr -nc nclust.xvg -mol

I get an error message saying that gromacs only finds 1 cluster but this is contradictory to what I am seeing when I viewed the trajectory.

Fatal error:
Lo: 0.000000, Mid: 1.000000, Hi: 1.000000

Can somebody please advise me on how to overcome this issue?

Many thanks,


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