Re: [AMBER] folding RNA using SGLD

From: Wu, Xiongwu (NIH/NHLBI) [E] <"Wu,>
Date: Tue, 30 Jun 2015 14:44:37 +0000

Hi Asmita,
SGLD will make the conformational search faster. Whether or not your RNA folds depends on the force field and simulation conditions, such as explicit or implicit solvent, temperature, etc.
SGLD (set with isgld=1) do have slight deviation in ensemble distribution while significantly enhance conformational search. SGLDg(set with isgld=3) can maintain ensemble distribution, but has reduced conformational search ability as compared with SGLD.
I would suggest to run SGLD (isgld=1, gamma_ln=1/ps, sgft=1) for your RNA folding. Once you can see your RNA fold, which indicate the force field and simulation conditions are OK, you can run SGLDg for an accurate folding simulation.
Please feel free to let me know if you have further questions.

From: Asmita Gupta []
Sent: Tuesday, June 30, 2015 10:11 AM
To: AMBER Mailing List
Subject: [AMBER] folding RNA using SGLD

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

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.

Please suggest n appropriate method as i couldn't find anything in the
literature using SGLD for RNA folding.


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Received on Tue Jun 30 2015 - 08:00:03 PDT
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