[gmx-users] Umbrella Pulling

[Justin A. Lemkul]

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

It depends on what you hope to demonstrate.  For instance, if you want to try to 
extract equilibrium thermodynamic information from SMD (which is inherently a 
non-equilibrium method), look into work by Jarzynski.

-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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