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

From: James Kress <>
Date: Sun, 19 Feb 2017 13:07:15 -0500


Does Amber contain code that allows the elimination of translation and
rotational degrees of freedom from the Hessian and /or gradient?


-----Original Message-----
From: David Case []
Sent: Saturday, February 18, 2017 3:34 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] [Amber] Frequencies from normal mode analysis in nab

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

AMBER mailing list

AMBER mailing list
Received on Sun Feb 19 2017 - 10:30:03 PST
Custom Search