[gmx-users] protein stability as a dimer
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 1 14:02:15 CEST 2010
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?
> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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