Steven Neumann wrote:
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
Dear Justin and Gmx Users,
I run a pulling of my ligand away from my protein with the same
mdp file and I obtained two different plots - Force vs time (The
breaking point occured at different times with different force).
Can you please explain?
If you change the stiffness of the spring, you change the magnitude
of the applied force. Thus, the behavior you see will occur either
faster or slower, depending on the strength of the spring.
-Justin
So how can I change the stiffness of my spring?
By changing pull_k1. I thought that's what you meant you had already done, but
I can see now that my interpretation wasn't correct. Understand the SMD is a
non-equilibrium, path-dependent process. I don't know what you're pulling from
what, but if the interactions are slightly different along the dissociation
pathway, the forces are different because the path is different.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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