Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy

From: David Case <david.case.rutgers.edu>
Date: Tue, 4 Apr 2017 21:44:22 -0400

On Tue, Apr 04, 2017, Ramin Salimi wrote:
>
> But I am a bit confused. When we calculate the total free energy of our
> system, we write it as Gtot = Eintra + Gsolv - TSintra , and we want to
> calculate the internal energy, we cannot unambiguously separate out the
> two contributions Eintra + Gsolv . Am I right? If so, can we say that
> the EGB shown in the output file of the GB/SA method is the sum of these
> two terms? or it is just Gsolv? If it just the Gsolv, how can we find
> the contributions solely from internal energy?

You can't separate EGB = Gsolv into internal energy and entropy components.
(Not sure if this answers your question or not....)

....dac


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Received on Tue Apr 04 2017 - 19:00:04 PDT
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