Re: AMBER: minimalization prior to nmode analysis, is it necessary?

From: Adrian Roitberg <>
Date: Thu, 05 Jan 2006 21:38:51 -0500

David A. Case wrote:
> On Wed, Jan 04, 2006, Magne Olufsen wrote:
>>but why should the snapshots
>>have to be minimized prior to nmode analysis?
> Conventional normal mode analysis assumes that the structure is at a minimum;
> none of the formulas for estimating vibrational entropies, etc. are correct
> if this is not the case.
> Operationally, having an RMS gradient of about 10**-4 kcal/mol-A (or even
> 10**-3) is usually enough to get results are are quite close to those you
> would get from a more precise minimum.
> ...dac
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to
Just to add my two cents to Dave's comments:
When the structure is fully minimized, the main approximation of the
theory of normal modes hold. This means that when the potential energy
is expanded to second order in cartesian coordinates, the first order
term in the expansion is exactly zero (the gradient is zero). When that
happens, you get 6 normal modes of zero frequency, NONE with imaginary
frequencies, and 3N-6 positive freqs.

If you do not minimize enough, you will see negative freqs. The trick is
to minimize enough to get 6 'very small' freqs and everything else
separated from that group. It is up to you to see what 'minimized enough
means' but I agree with Dave 10**-3 (-4) might be enough.

Why is this important ? Because fluctuations for instance, depends like
1/freq^2 of the nmode frequency. So, errors in the small freqs could
give large errors in fluctuations.

One more caveat: there is a full body of literature talking about
instantaneous normal modes, where you do nmode without minimization in
snapshots from MD. See papers by Tom Keyes for instance. That is a
different set of ideas that 'regular nmodes, but share some background.

I hope this helps.

                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email
To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
   --  Theodore Roosevelt
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Jan 06 2006 - 02:42:03 PST
Custom Search