[gmx-users] PCA analysis

[Ashu Sharma]

Dear all,

I am trying to perform the principle component analysis of my protein
simulation. Eigen vectors 1-4 cover more than 60 % of fluctuations. When I
use -filt option with -b, -e and -skip flags in gmx anaeig, I get an
ensemble which represents the fluctuation with the specified intervals (-b
and -e) at desired frequency (-skip).

What I want to know is that whether the coordinate frames which I get with
the above mentioned approach, really come from time points in the
trajectory? Like, if I take a single model from the filtered ensemble,
would there be a frame in the trajectory with zero rmsd to this frame OR
these filtered frames are 'altered coordinates' from the simulation
trajectory to reflect motions calculated by Eigen vectors?

Any clarification or reference to the source where I can read more about
this would be highly appreciated.

Thanks a lot !

Best,
Ashu