I have results from the MDS and I want to cluster them. what are the best methods, and clustering parameters to use? and is there a webserver of open-source programs that can do this?
Thank you very much
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.
UCSF Chimera is indeed a good choice.
https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html
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