From: Abramyan, Tigran (
Date: Fri Sep 02 2016 - 12:27:59 CDT

Dear Sir/Madam,

I would like to understand the following regarding the Cornell clustering plugin in VMD:

1. I understand that the metric used is RMSD, however, what is the underlying clustering algorithm? Agglomerative hierarchical (single-, average-, complete-, ward-linkage, etc.), divisive, kmeans?

2. Is there a way to select the optimal number of clusters instead of randomly picking a value for 'Num: ' in the VMD GUI?

3. What is 'none (..)'? Are those outlier frames? Why don't they belong to clusters?



Tigran M. Abramyan, Ph.D.
Postdoctoral Fellow, Computational Biophysics & Molecular Design
Center for Integrative Chemical Biology and Drug Discovery
Eshelman School of Pharmacy
University of North Carolina at Chapel Hill
3219 Marsico Hall, Campus Box 7363
125 Mason Farm Road
Chapel Hill, NC 27599-7363