[gmx-users] Clustering

[Pandya, Akash]

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,

Akash