[gmx-users] Clustering

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Thu Aug 3 11:05:34 CEST 2017

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 create a separate tpr file for the molecule of interest. And I had to generate another trajectory file in order for them to match.  I run the command below:

gmx clustsize -f glycine.xtc -s glycine.tpr -nc nclust.xvg -b 0 -e 60000 -cut 0.35 -mol

I get an error message saying that gromacs only finds 1 cluster but this cannot be right as I can see more than one cluster forming during the simulation

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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