AMBER Archive (2009)

Subject: Re: [AMBER] What is the meaning of IED values for PCA analysis?

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Aug 05 2009 - 11:39:30 CDT

On Mon, Aug 03, 2009, Catein Catherine wrote:
>
>
> When we open the vector and projection for the PCA analysis, I found the
> vector values stop at 35, but the sliders can move from -20 to 40. What
> is the physical meaning of these values? When we report the magnitude
> of the vector, which number should we use?

The magnitude on the slider is an arbitrary number, and doesn't really have a
physical meaning. The only way I really know to calibrate it would be to
compute the energy as a function of vector magnitude, then report how much
energy strain you have added (relative to the starting point), by moving to a
certain displacement.

...good luck...dac

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