[gmx-users] anomalous eigenvector in PCA (Principal Component Analysis)

[Justin Lemkul]

On 12/27/15 6:48 PM, Nima Soltani wrote:
> Hi
> 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 :
> https://app.box.com/s/e6b87ar9j75q227qe6sx1udeyqdszgdl
> ​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

-- 
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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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