On Wed, Feb 02, 2011, Jakob Luchner wrote:
>
> I did an simulation of a short b-dna molecule (7 basepairs). After
> simulating I calculated the total energy and bonding energies (VdW,
> elec etc) with namdenergy. The energies don't match with the energies
> calculated by amber and listed in the out-files. The discrepancy is
> about 10%.
Be sure to check the "caveats" list on this page:
http://www.ks.uiuc.edu/Research/namd/2.7/ug/node14.html
We are in the process of putting together a more detailed discussion of how to
get the same energies in namd and Amber, but it can be a rather tricky thing.
If people on the list have examples that work (or that don't work) it might be
worthwhile giving your experiences.
...thx...dac
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Received on Wed Feb 02 2011 - 11:00:06 PST
