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

Justin Lemkul jalemkul at vt.edu
Mon Dec 28 02:39:47 CET 2015

On 12/27/15 7:08 PM, Nima Soltani wrote:
> Justin Lemkul <jalemkul at ...> writes:
>> 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
> Thank you Dear Dr. Lemkul for your reply
> Actually it is a portion of Alzheimer's A-Beta peptide, i.e. simulated in
> different environments, each simulation is approximately 100ns long.

I doubt that's enough to get any sort of converged data for such a system to do 
reliable PCA.

> In those simulations A-B adsorbs to different surfaces and in it's adsorbate
> state has only a few conformationally allowed states.
> not every eigenvector looks as bizarre as this one.
> Could it be wrong choice of reference structure that caused this ?

The eigenvector seems to correspond to an elongation along the peptide's 
sequence.  There's nothing wrong with that.  The N-terminal residue or two look 
a bit bizarre, likely due to rapid, local conformational changes, the kind that 
wouldn't impact the overall conformation of the peptide but will show up in this 
kind of analysis.



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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