[gmx-users] PCA, equilibrium, free energies

Y. U. Sasidhar sasidhar at chem.iitb.ac.in
Fri May 5 12:14:18 CEST 2006

We performed a long simulation on a peptide and we have carried out
principal component analysis. First three eigen vectors account for 70% 
of the variance. From 5th eigen vector onwards distributions are 
gaussian. The first eigen vector definitely is not a gaussian. Under 
these conditions ***can free energies be derived ?** from eigen vector1 
versus eigen vector2 contour plots or from distribution of points in 
space spanned by eigen vectors 1,2,3 as done by :

1)Daidone I, Amadei A, Di Nola A.Thermodynamic and kinetic
characterization of a beta-hairpin peptide in solution: an extended phase
space sampling by molecular dynamics simulations in explicit water.
Proteins. 2005 May 15;59(3):510-8.

2)Ikeda K, Higo J. Free-energy landscape of a chameleon sequence in
explicit water and its inherent alpha/beta bifacial property. Protein Sci.
2003 Nov;12(11):2542-8.


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