Re: [AMBER] Free Energy Calculate

From: David A Case <>
Date: Mon, 5 Mar 2012 08:24:28 -0500

On Mon, Mar 05, 2012, mehdi bagherpoor wrote:
> How I could calculate *free Energy* of DNA in presence of ions and water
> molecules (*explicit water*)?

There are lots of ways to calculate (changes in) free energy; you might start
with the chapter entitled "Sampling and free energies" in the Amber manual.

> In the values *Etot* and *EKtot* and *EPtot* (file *md.out*), is
> energy of water molecules calculated?



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Received on Mon Mar 05 2012 - 05:30:03 PST
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