Re: [AMBER] Obtain dynamical matrix away from equilibrium

From: Adrian Roitberg <>
Date: Thu, 9 Feb 2017 13:10:48 -0500

You do not need to minimize in nab.

Just read the structure, and compute the normal modes without the
minimization step.

Now, I am not sure how nab reports the imaginary frequency modes, but it
should be easy to check.


On 2/9/17 1:00 PM, The Cromicus Productions wrote:
> Hi everyone,
> I'm performing some non-equilibrium simulations and would like
> to obtain the instantaneous normal modes (diagonalizing the dynamical matrix
> at different configurations). Any idea of how to do this?
> Using normal mode analysis (as in nab) is out of question because
> that pulls my configuration into the equilibrium during the minimization.
> Since now thanks for any clue you may provide me.
> Regards,
> Sebastian
> _______________________________________________
> AMBER mailing list

Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
AMBER mailing list
Received on Thu Feb 09 2017 - 10:30:03 PST
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