Re: [gmx-users] protein stability as a dimer

[Justin A. Lemkul]

sonali dhindwal wrote:
Hi Justin,

Sorry for the mistake, I wrote 0.1 ns in
"still there are more fluctuations but and it decreses again to 0.28 nm 
at 0.1 ns."
it is 1 ns instead, I ran the simulation for 1ns.


I still would call that a fluctuation, and nothing abnormal.

I have put the job to run for 1 more ns, so may be there I could analyse 
something as u said.

Here's a tip - plan your timeframe before starting your simulation so you're not 
guessing.  2 ns is likely insufficient to convergence of many properties of a 
large system as well.  Maybe RMSD, but other more sensitive properties maybe 
not.  What does the literature tell you about the length of similar systems?

-Justin

Thanks a lot.

--
Sonali Dhindwal


--- On *Thu, 1/7/10, Justin A. Lemkul /<jalem...@vt.edu>/* wrote:


    From: Justin A. Lemkul <jalem...@vt.edu>
    Subject: Re: [gmx-users] protein stability as a dimer
    To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
    Date: Thursday, 1 July, 2010, 5:17 PM



    sonali dhindwal wrote:
     > Hello All,
     > I have done simulation for 1ns on a protein dimer using GROMOS96
    43a1 force field.
     > I want to study if the protein is stable as  a dimer or not, so
    can you please give me some suggestion as to what analysis  I could
    do for the same.
     > I checked g_rms after the simulation, graph which I am getting is
    like, first rmsd is increases rapidly to 0.2nm for for 0.1 ns and
     > then till 0.8 ns it still increased to 0.3 nm and
     > still there are more fluctuations but and it decreses again to
    0.28 nm at 0.1 ns.
     >
     > So what could i infer about the stability of the protein as a
    dimer from this data.

    If you've only done 100 ps of simulation, not much.  I would also
    question why you consider it a "decrease" from 0.3 nm to 0.28 nm
    rather than just a fluctuation.  Run a longer simulation to gather
    meaningful RMSD values.

    As for other analysis to do, do some homework in the literature, and
    also consider your own goals for running the simulation.  Certainly
    you have a purpose.

    -Justin

     > Thanks in advance.
     > Regards
     >
     > --
     > Sonali Dhindwal
     >
     >

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

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

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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