Hi,

Gromacs tools can help you.

http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-cluster.html

Martiniano Bello I am using NAMD for simulation. Do I need to use Gromacs so I can use this tool?

Hello Ibrahim M. Ibrahim

If you used GROMACS for your MD simulation then you can use the method suggested by Martiniano Bello .

However, since you are using NAMD, maybe you can use UCSF Chimera to cluster your trajectories. All the best.

Thank you very much Farrah Wahidah Ridzwan

Hi,

Ok, you can also use LOOS.

http://loos.sourceforge.net/

UCSF Chimera is indeed a good choice.

https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html