[AMBER] Units from quasiharmonic analysis of Principal Components

From: German P. Barletta <pbarletta.gmail.com>
Date: Sun, 19 Jul 2020 13:48:38 -0300

Hi everyone!

I know from Case's paper on crambin, and this mailing list, that when
running this kind of analysis with cpptraj (that is, using the matrix
mwcovar command), eigenvalues are reported in units of cm^-1. Why is that?
It's supposed to be a diagonalization of a covariance matrix, so the
eigenvalues should be in units of distance^2 (say, cm^2). Right? Is Amber
just taking the inverse square and reporting those values? If so, why? Or
is there something else I'm missing?

I'd be grateful for any insight. Stay safe!
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Received on Sun Jul 19 2020 - 10:00:03 PDT
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