So how do I calculate the internal energy of my DNA molecule?
I used explicit solvent model to stretch my DNA, and now I want to calculate the internal energy during the extension. But I cannot get the internal energy out of solvated trajectory since it is dominated by solvent contribution from the individual water molecules. So I strip water molecules from the trajectory and run GB/SA.
But I don't know how to find the internal energy?
Ramin
Sent from my Windows Phone
________________________________
From: David Case<mailto:david.case.rutgers.edu>
Sent: ý4/ý4/ý2017 8:44 PM
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy
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 - 19:30:02 PDT
