[gmx-users] anomalous eigenvector in PCA (Principal Component Analysis)
jalemkul at vt.edu
Mon Dec 28 00:56:30 CET 2015
On 12/27/15 6:48 PM, Nima Soltani wrote:
> I have performed principal component analysis by using g_covar module of
> Gromacs 5.0 (Peptide's backbone atoms were selected both for least square
> fit and covariance analysis)
> then 2 extreme conformations along different eigenvectors derived by
> "g_anaeig -extr"
> The resulting structure look likes this :
> Is there any way to correct those artifices that can be observed in the
> peptide backbone?
Looks to me like you're just analyzing a highly polymorphic peptide. Maybe
there's nothing even useful to conclude from such analysis. How long is the
simulation? What do you know about the conformational ensemble you've
simulated, and how well it is converged?
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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