[gmx-users] Projection of trajectory onto PCs

[tarak karmakar]

 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