[gmx-users] Projection of trajectory onto PCs

[Tsjerk Wassenaar]

Number ii)

Cheers,

Tsjerk
On Dec 30, 2014 12:57 PM, "tarak karmakar" <tarak20489 at gmail.com> wrote:

>  Dear All,
> Could anyone please elaborate 'projections of trajectory onto first two
> principal components' in PC analysis?
>
> Projection of trajectory onto first two eigenvectors- Does it mean that
>
> i) the superposition of molecular structures (a set of C-alpha coordinates)
> over a trajectory are projected onto a plane defined by first two
> eigenvectors?
>
> or
>
> ii) the numbers (in 2D projection plot, obtained from g_anaeig) are the
> results of the dot products of displacement vectors of the C-alpha atoms
> with each of the principal eigenvectors?
>
>
> Thanks and regards,
>
> Tarak
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