[gmx-users] Cluster analysis on molecules

[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 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,

Akash