Re: [AMBER] folding RNA using SGLD

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 30 Jun 2015 11:30:40 -0400

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 Tue Jun 30 2015 - 09:00:02 PDT
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