Re: Convergence of Sampling and Deciding on Simulation Length

From: Nikolaos Glykos (
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
 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) 
     Ext.77620, Tel (lab) +302551030615,

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