AMBER Archive (2004)

Subject: Re: AMBER: the energy difference between sander and nmode

From: David A. Case (
Date: Fri Nov 12 2004 - 16:43:28 CST

On Fri, Nov 12, 2004, xiaowei li wrote:

> I have used SANDER (amber 8) and NMODE (amber 7) to minimize the
> energy of poly[C]-poly[G] RNA with 12 base pairs without sodium ions. It
> seems to me that the energies after minimization are different.

It is certainly possible that you have converged to two different local minima
in the two simulations. You should test the _same_ coordinates in the two
programs to see whether or not they give the same energies.

(Why are you using scee=2.0? This is only appropriate for very old force

...good luck...dac

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