Thanks again
There is only one question left that I cannot answer.
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 that graph?
Thanks
Ramin
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Saturday, March 25, 2017 1:31:03 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Force/Energy vs extension curve from Steered MD
The protocol in that paper is completely different than yours.
I strongly recommend you find some more recent papers for DNA
stretching, that one is pretty old.
The key sentence in their paper showing the difference with what you are
doing is in:
"The DNA molecule was stretched by increasing the distance between the
two restrained atoms by 1 Å followed by an intervening 10 ps relaxation
period."
You are pulling continuously without the relaxation step.
Also, what they are plotting is the derivative of the potential energy
vs distance to get the force, while the force column in your table is
the instantaneous force during your pulling.
In your simulation, column 4 is NOT the energy, but rather the WORK,
which is a completely different object.
Adrian
On 3/25/17 2:15 PM, Ramin Salimi wrote:
> Molecular Dynamics Simulations of Duplex Stretching Reveal the Importance of Entropy in Determining the Biomechanical Properties of DNA
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7Ceb0f0ed71f234b974af508d473ad249c%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636260634862185894&sdata=9ruyEThMqvXkX8p3CP3AYL38W3QXbyTk0nUr3zNwX3k%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 26 2017 - 14:30:02 PDT
