[AMBER] [Amber] Frequencies from normal mode analysis in nab

From: The Cromicus Productions <thecromicusproductions.gmail.com>
Date: Tue, 14 Feb 2017 03:03:38 -0500

Hi everyone,

I have a question about nab. I see that, when doing normal mode analysis,
some of the first rows only have two columns instead of five in the output
printed in the screen. Does this mean that those frequencies are the rigid
body motions?
In particular, if I have 3 modes with frequency 0 and two columns, and then
the fourth mode has a frequency 0.0002 but five columns, can I assume that
that mode is not a rigid body motion?
Thanks a lot!


P.S.: I'm working away from the equilibrium position so I usually have a
lot of 'negative' frequencies, some zero, etc.. so, I would like to have a
quick way to eliminate the rigid body motions without looking at each
vector. The number of columns from the printed output seemed promising
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Received on Tue Feb 14 2017 - 00:30:02 PST
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