AMBER Archive (2006)

Subject: Re: AMBER: identical high energies

From: Thomas Cheatham (
Date: Thu Aug 17 2006 - 21:57:23 CDT

> I am working with two slightly different conformations
> of the same structure. I solvated each structure in
> XLeap or TLeap and then subjected them to energy
> minimizations. Something very strange happened: the
> first energy of each run is extremely high, and this
> first energy is identical between the two runs (even
> though the components of the energy are different).
> See below:
> Conformation 1:
> 1 1.0240E+16 1.5897E+15 6.9165E+17
> VDWAALS = ************* EEL = -764301.4029
> Conformation 2:
> 1 1.0240E+16 1.5902E+15 6.9165E+17
> VDWAALS = ************* EEL = -764246.3698

The similarity is likely all due to the van der Waals... ***'s are
printed since this is beyond the FORMAT specification as it is a large
number and the VDWAALS is not printed with x10**X notations.

If you look at any of the differences in the energy you see, these are all
in the E+06 to E+07 range yet your total energy is E+16! Likely the same
problem with the first structure in overlap is operative in the second
such that both lead to 10 peta-kcal/mol energetics.

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