Thanks Bill.
But can you please elaborate why minimization, and why in vacuum?
What do you mean by single-point?
Thanks
Ramin
Sent from my Windows Phone
________________________________
From: Bill Ross<mailto:ross.cgl.ucsf.edu>
Sent: ý4/ý4/ý2017 11:18 PM
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy
A single-point energy minimization in vacuum would give you an internal
energy.
Bill
On 4/4/17 7:13 PM, Ramin Salimi wrote:
> 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 Wed Apr 05 2017 - 03:30:02 PDT
