[gmx-users] Umbrella Pulling

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Steven Neumann wrote:
> 
> 
> 
>         On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto: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
> 
> 
> I used exactly the same mdp file with the same parameters - the same 
> same pull_k1 as well and I obtained different plots. The starting 
> configuration is also the same. I pull a ligand away from the protein.
>  Would you obtain from two normal MD or SMD simulations with the same 
> starting configuration different results?
> 

Yes, it's quite possible.  MD is a chaotic process.

http://www.gromacs.org/Documentation/Terminology/Reproducibility
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation

-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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