[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 /<jalemkul at vt.edu>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] protein stability as a dimer
>     To: "Discussion list for GROMACS users" <gmx-users at 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

========================================