Re: [AMBER] folding RNA using SGLD

From: Asmita Gupta <asmita4des.gmail.com>
Date: Thu, 2 Jul 2015 18:19:02 +0530

Thanks Jason and Xiongwu, for the suggestions.

On Tue, Jun 30, 2015 at 9:00 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Tue, Jun 30, 2015 at 10:11 AM, Asmita Gupta <asmita4des.gmail.com>
> wrote:
>
> > Dear users,
> >
> > I am trying to study folding pathway of an RNA chain. Starting from an
> > extended conformation, the chain should adopt a pseudoknot structure. I
> > don't expect that the structure should ultimately fold into its native
> > conformation.
> >
> > Is self-guided langevin dynamics is a good idea to study this kind of
> > process. There are studies using Temperature replica exchange, but as far
> > as i have read, it involves reweighing to get canonical ensemble, while
> > this issue is not there with SGLD.
> >
>
> ‚ÄčThis isn't to say that temperature REMD is better than SGLD, but you don't
> actually need to reweight T-REMD simulations to get the proper canonical
> ensemble. You can just extract the trajectory at the temperature you want
> to analyze, and the canonical ensemble at that temperature should already
> be correct.
>
> You can always reweight the higher-temperature replicas to add *more*
> information (and improve the convergence of your ensemble) to the
> low-temperature structure (using something like MBAR), but that's not
> strictly necessary.‚Äč
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Jul 02 2015 - 06:00:03 PDT
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