Hi Bill
I am actually trying to plot internal energy vs extension of DNA. In fact, I have stretched DNA molecule in explicit solvent water. Now, I want to plot internal energy vs extension reproducing Fig. 2 of the following paper:
Molecular Dynamics Simulations of Duplex Stretching Reveal the Importance of Entropy in Determining the Biomechanical Properties of DNA
Sarah A. Harris,* Zara A. Sands, and Charles A. Laughton
In Fig. 2, they have plotted internal energy vs extension through GB/SA implicit solvation model. But when I apply GB/SA, it only gives the free energy of solvation as EGB. In the paper, it explicitly mentions that Fig. 2 is the internal energy vs exension.
But how to get that?
Thanks
Ramin
________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Wednesday, April 5, 2017 12:35:51 PM
To: AMBER Mailing List
Subject: Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy
Hi Ramin,
I was loosely adopting the single point term from quantum mechanics,
i.e. you do not need to minimize, just get the energy at the first step.
One does it in vacuum in order to restrict the total energy to the
internal energy of the molecule.
Perhaps if you mention what you want to do with the number, others can
comment on how meaningful it is; it doesn't seem to be sought often.
Bill
On 4/5/17 3:01 AM, Ramin Salimi wrote:
> 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 - 20:00:02 PDT
