[gmx-users] story behind the PCA

[Justin Lemkul]

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

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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
http://mackerell.umaryland.edu/~jalemkul

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