# [gmx-users] Re: PCA depends of the number of frames?

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 26 14:57:49 CEST 2011

```On 26/09/2011 10:54 PM, Ricardo Cuya Guizado wrote:
> Thanks Tsjerk
>
> >> PCA depend of the number of frames?
>
>
> >Yes, it does. This has, in fact, been pointed out in the early papers
> on PCA in MD
>
> Please, Would you give me some references,

See manual section 8.10 and references, or the references in the
literature of work similar to that which you intend to do...

Mark
>
>
> Ricardo
>
>
> Hi Ricardo
>
> > For the case (1) and (2) the most representative structure was used
> in the
> > option -s ( One that has the lowest rmsd with respect to the average
> of each
> > cluster).
> > In case (3) the initial structure of the MD was used in the option -s.
>
> If all belong to the same system, it is better to use one reference
> structure, to define the conformational space in the same way,
> allowing direct comparison.
>
> > When I look the eigenvalues for the case (1) and (2), I found that the
> > eigenvalue is zero only after index="number of frames" (see below)
> > In the case (3) the distribution is smooth
> > I could expect a similar distribution for the case (1) and (2),
> because the
> > frames are representative of the dymanics of the protein.
> > Why this difference?
> > PCA depend of the number of frames?
>
> Yes, it does. This has, in fact, been pointed out in the early papers
> on PCA in MD. I think it's best to read up more about PCA, including
> some introductory material from statistics. One thing I'll give away
> though... ;) Consider the motion of a particle in three dimensions. If
> you have two frames, you can say something about motion along a line.
> You need two frames to say something about motion in a plane, and you
> need at least three points to say something about motion in all three
> dimensions. Now in your case, each conformation is one point and the
> conformational space in which the point moves has 3N dimensions. If
> you have two points, you can only say something about motion along a
> line, i.e., you have one component with nonzero eigenvector. With
> three points (conformations), you can obtain two eigenvectors, which
> span a plane, etc.
>
> Hope it helps,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>

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