[gmx-users] Umbrella Pulling

[Steven Neumann]

On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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/Terminology/Reproducibility>
> http://www.gromacs.org/**Documentation/How-tos/**
> Extending_Simulations#Exact_**vs_binary_identical_**continuation<http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation>
>
> -Justin
>
>
Like in a real experiment :) In this case it is required to run a lot of
simulations with the same parameters to be able to exract desired values?
Thank you 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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