Hi Ramin,
1-step minimization in vacuum is as good as it gets I believe.
Bill
On 4/5/17 7:54 PM, Ramin Salimi wrote:
> 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 Thu Apr 06 2017 - 01:00:03 PDT
