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?
yes.
...dac
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Received on Mon Mar 05 2012 - 05:30:03 PST
