AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 05 2006 - 19:56:26 CST

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

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