VMD-L Mailing List
From: Abramyan, Tigran (tigran_at_email.unc.edu)
Date: Fri Sep 02 2016 - 12:27:59 CDT
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 Email: tigran_at_email.unc.edu