From: Nikolaos Glykos (glykos_at_mbg.duth.gr)
Date: Tue Jul 16 2013 - 12:16:12 CDT
> How do we decide whether our simulation has run long enough for the
> PCA and EMD
> analysis to be of any relevance? For example, cosine content of a
> trajectory ...
Concerning PCA, I would rather use eigenvector overlap instead of
cosine content.
See "Quantifying uncertainty and sampling quality in biomolecular
simulations",
Annu Rep Comput Chem. 2009 Jan 1;5:23-48.
--
Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office)
+302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
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