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

From: David Case <>
Date: Sat, 18 Feb 2017 15:33:57 -0500

On Tue, Feb 14, 2017, The Cromicus Productions wrote:
> 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?

Probably: but they also have zero frequency, so the code doesn't try to
compute any thermodynamic functions for them, which is why the extra columns
are blank.

> 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?

A very small non-zero frequency is probably still a rigid body mode. As noted
above, the printing of the extra columns is just based on the frequency, not
on any analysis of the character of the modes.

> 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

I'd look at the frequencies, not the number of columns.

...good luck...dac

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Received on Sat Feb 18 2017 - 13:00:03 PST
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