Maybe quantum methods would be better actually, I wouldn't know, but it
would be interesting to compare the curves for a variety of potentials.
It seems molecular mechanics force fields like Amber are adapted to less
stressful situations, and I'd think quantum methods should adapt better,
but I am not at all an expert on that. It is relatively easy to get the
vacuum (internal) energies with Amber at least.
Bill
On 4/6/17 12:41 AM, Bill Ross wrote:
> 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 - 02:00:02 PDT
