Re: [AMBER] Question about PCA tutorial

From: Abhilash J <>
Date: Thu, 30 Apr 2020 19:03:54 -0400

Hi Thomas,

    Thanks for clarifying the doubt. It was quiet helpful.




On Wed, Apr 29, 2020 at 11:24 PM Thomas Cheatham <> wrote:

> > I have a question on PCA. I did AMBER PCA tutorial and i have a
> > question. How to decide how many vectors to use. The PCA tutorial uses 3.
> > ( runanalysis diagmatrix cpu-gpu-covar out cpu-gpu-evecs.dat vecs 3
> name
> > myEvecs nmwiz nmwizvecs 3 nmwizfile dna.nmd nmwizmask :1-36&!.H= )
> Well, no one has responded yet so I will give it a shot noting that
> hoefully my people will correct me if I am wrong.
> Like clustering, there is no right answer and it depends upon what you
> want to learn. When I teach about PCA, I try to start from the concepts of
> normal modes of motion. You do a QM minimization and you can visualize the
> normal modes. The first eigenvalues/eigenvectors report on the slowest
> collective modes of motion (the overall molecule bending / twisting with
> many of the atoms moving). The later ones, the high frequency modes, are
> just a couple of atoms moving, such as bond vibrations. If you haven't
> ever viewed modes of motion in GaussView or equivalents, do...
> When looking at the modes of motion from PCA, they are ordered from low
> frequency to high (bonds). Bond vibrations do not tell you much about the
> dynamics or function or really much more than the fact that the bond is
> vibrating. Often the most informative are the first few modes on motion
> since they give you a picture of the largest / collective motion. The
> first few modes represent 90% of the motion. So, back to your question
> about how many modes you need to see depends on what you are trying to
> learn.
> In the papers you reference from my lab, we were trying to demonstrate
> reproducibilty and convergence from independent simulations from different
> initial conditions. If different simulations showed equivalence for the
> first three modes of motion, probably good. If 15-20 modes agree (between
> independent simulations) even better since this gets to ~95-99% of motion
> -- hard to claim independent simulations are not equivalent if they
> reproduce 15-20 of the modes. Does this guarantee convergence, no, since
> the independent simulations could have both missed important states (i.e.
> locally converged, not necessarily globally converged). Yet, do we need to
> compare all modes, probably not (noise) but we could with CPPTRAJ since it
> was designed by be flexible (allow you to investigate what you want).
> CPPTRAJ by being flexible means experiement; there is no one "correct" way
> and the rate limiting step in simulation these days is not running MD, but
> figuring out what the MD means.
> To reframe your question, it is not about the number of modes, it is what
> question are you trying to answer with respect to the modes of motion?
> --tec3
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Received on Thu Apr 30 2020 - 16:30:03 PDT
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