[gmx-users] Umbrella Pulling

[Steven Neumann]

On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul <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>> 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?

Steven


> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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