[gmx-users] story behind the PCA
jalemkul at vt.edu
Tue Nov 15 02:42:35 CET 2016
On 11/14/16 6:21 AM, Seera Suryanarayana wrote:
> Dear gromacs users,
> I have gone through many tutorials and I didn't get much about
> principal component analysis(PCA) in gromacs. Kindly some one tell me
> the story behind the PCA and whats the relation between PCA and free
> energy landscape?
One can construct free energy surfaces from any two variables, but the first two
eigenvectors from PCA are frequently chosen as they reflect the dominant,
underlying motions that quantify conformational changes. As such, this is a
logical approach to building free energy surfaces, e.g. the probability that
given conformations in the trajectory occupy different energy basins on the surface.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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