[gmx-users] Umbrella Pulling

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at 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

-- 
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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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