AMBER Archive (2005)

Subject: Re: AMBER: Alignment tensor and Interia tensor

From: David A. Case (case_at_scripps.edu)
Date: Sat Dec 03 2005 - 13:05:30 CST

On Sat, Dec 03, 2005, RadhaKumari Yadav wrote:
>
> When I did residual dipolar refinement using sander there are two lines
> in output like: "Diagonalize the alignment matrix" and "Diagonalize the
> moment of interia tensor". I am bit confused about this. According to me
> alignment tensor should be same as Inertia tensor. Can anyone clarify my
> doubt.

I don't know why you think the two tensors should be the same. The inertia
tensor is just defined by the structure; the alignment tensor depends upon the
physical mechanism causing the alignment (steric, electrostatic, magnetic).
Amber of course doesn't know anything about what is causing the alignment, and
is just reporting a value that is fit to the input NMR data.

...dac
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