Re: AMBER: Free energy for part of the system

From: David A. Case <>
Date: Tue, 4 Dec 2007 10:37:16 -0800

On Tue, Dec 04, 2007, jialei wrote:
> We would like to compare free energies between two
> duplexes (one target duplex and one control). The reason why we thought out
> computing the central 5mer free energy is that there are end effects during
> the simulation, while the central 5mer looks normal.

Do the target and the control have the same sequence? If not, I don't see how
you can make a meaningful free energy comparison. And if they do have the
same sequence (so that the differences are in the non-central base pairs), I
don't see how you would interpret the result (although you could certainly
calculate it in the manner you suggest).


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Received on Wed Dec 05 2007 - 06:07:30 PST
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