Hi,
You could always post-process your trajectories using 'sander' and the
namelist variable 'imin=5'. See the manual for full details.
-Dan
On Tue, Apr 4, 2017 at 10:13 PM, Ramin Salimi <ramin.salimi01.utrgv.edu> 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: 4/4/2017 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Apr 05 2017 - 09:30:04 PDT
