AMBER Archive (2005)

Subject: Re: AMBER: E of amber calculations

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Dec 15 2005 - 06:30:08 CST


> Anyway, my ultimate question is if there is a way that we can simply
> compare stability/ energy of current conformation of the molecule.
>
not without averaging over all of the water configurations or else
replacing them with a continuum model. These are energies of the
entire system, not just the DNA.

> with big thanks in advance,
>
> Young Jin

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