Re: [gmx-users] Umbrella Pulling

[Justin A. Lemkul]

Steven Neumann wrote:


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



    Steven Neumann wrote:



        On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:



           Steven Neumann wrote:



               On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul
               <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
               <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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

--
========================================

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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