AMBER Archive (2006)

Subject: Re: AMBER: About the unit of the projection onto eigenvectors

From: David A. Case (
Date: Fri Jan 27 2006 - 16:20:17 CST

On Tue, Jan 17, 2006, zgleo wrote:

> I have used ptraj to perform PCA analysis, and obtained the projection
> onto a few eigenvectors. However, the projection values seem vary too
> much (around -30 to +50) for the unit of "angstrom". If not, could
> anybody tell me what is the unit of the projection values?

Your expectations about the behavior of the projections may be wrong. The
numerical values depend upon the normalization of the eigenmodes. You can
check the results by reconstructing the trajectory: for any snapshot "s(t)",

     s(t) ~ a1(t)*q1 + a2(t)*q2 + a3(t)*q3 + .....

Here a1, a2, a3 are the projections, and q1, q2, q3 are the modes in the
"modesfile" file. The magnitudes of the a1 coefficient might look large
because the (normalized) q1 vectors have pretty small elements. So when a1(t)
varies by a lot, it doesn't necessarily mean that the protein is moving a lot.

[Does any ptraj guru know of a test case or demo that iilustrates the
"projection" command?]

...hope this helps...dac

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