Hi Jason
Thanks for the reply
The following is the paper whose result I am trying to reproduce:
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
First question is a general question: I am not justified quite well what the difference is between using jar option, using nmropt, and using ncsu in pulling the molecule? I mean is there any major difference among the output files of these after pulling?
second question is on the aforementioned paper. When we pull the molecule, then like force vs extension, we want to plot INTERNAL ENERGY vs extension, but we cannot calculate the internal energy of the DNA with solvated trajectories because it is dominated by the solvent contribution from individual water molecules. How do we plot INTERNAL ENERGY vs extension?
Thanks
Ramin
________________________________
From: Jason Swails <jason.swails.gmail.com>
Sent: Sunday, March 26, 2017 7:27:26 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Force/Energy vs extension curve from Steered MD
On Sat, Mar 25, 2017 at 3:05 PM, Ramin Salimi <ramin.salimi01.utrgv.edu>
wrote:
> Adrian
>
> That was very informative answer. Thanks very much.
>
> However, I do have questions as well: They should have used nmropt not
> jar. There seems to be nothing as relaxation period within the nmropt
> codes. It seems to me that they wrote a loop script to pull the DNA for 1
> A0, do the relaxation period; then stretch it one more unit, and it goes on
> to reach 110 A0. Am I right?
>
> Secondly, Column 4 being the work but I said the derivative of column 4 vs
> column 1 should give the force vs extension was due to the relation
>
> Work Done=Force*Displacement
>
> I thought that the force coming from the potential energy should be the
> same force in the above relation. Is that right?
>
It's unclear what you mean by "the force coming from the potential
energy". The Work that Adrian is referring to is the work done by the
restraining potential as it moves. This is a non-equilibrium,
path-dependent quantity (i.e., it is not a state function and will vary --
often by large amounts -- from one simulation to the next.
You *can* get back to state variable quantities from non-equilibrium work,
but only if you run ensembles of simulations and employ relations like the
Jarzynski equation (which is why the variable in Amber is named "jar").
So the take-home message here is that none of the energies you calculate
from a single Steered MD simulation is meaningful -- only when combined
with many SMD simulations via the Jarzynski equation do the reported works
become meaningful.
HTH,
Jason
--
Jason M. Swails
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Received on Sun Mar 26 2017 - 22:00:03 PDT
