[gmx-users] protein stability as a dimer

sonali dhindwal sonali11dhindwal at yahoo.co.in
Thu Jul 1 13:59:08 CEST 2010

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


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

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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