Re: [AMBER] RNA Simulation

From: Jiri Sponer <>
Date: Thu, 12 Mar 2015 20:16:10 +0100 (MET)

Dear Jacob,

it is rather impossible to PREDICT 3D structure by
atomistic simulations (you need to compare the time
scale of the simulation with the time scale of real

Look into these papers, where we discuss such problems.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to
the Ribosome. Journal of Physical Chemistry Letters, 5, 2014, 1771-1782.

Computer Folding of RNA Tetraloops? Are We There Yet? Journal of Chemical
Theory and Computation, 9, 2013, 2115-2125.

Molecular dynamics simulations of G-DNA and perspectives on the simulation
of nucleic acid structures. Methods, 57, 2012, 25-39

In principle, unbiased (standard) simulations mimic real dynamics
of the molecules from a given starting structure so, 100 ns is 100 ns.
There are enhanced sampling methods, but they introduce additional
nontrivial approximations, collective variables etc.


On Thu, 12 Mar 2015, jacob wick wrote:

> Date: Thu, 12 Mar 2015 23:58:59 +0530
> From: jacob wick <>
> Reply-To: AMBER Mailing List <>
> To:
> Subject: [AMBER] RNA Simulation
> Hi all,
> I am trying to simulate a chunk of RNA molecule (20 residues) to predict
> its tertiary structure. The crystal structure of that RNA is not available,
> so I don' t know how that chunk will finally look like.
> I am creating that 20 residues chuck by NAB and then I am simulating it for
> 100 ns as per the AMBER TUTORIAL B1 with (ht tp://
> force filed. Within few ns, I am getting a
> pseudoknot structure, after which tere is no significant change in rmsd.
> The rmsd difference between the initial structure (created by NAB) and the
> md average structure is around 52 (after re-imaging by cpptraj) which is
> constant from 5ns to rest of the simulation period.
> Please suggest what can I do to make my RNA simulation more reliable. Is
> the protocol used by me is right?
> Can I justify the huge change in the rmsd as I am starting with a streach
> created by NAB and finally I am getting a stable tertiary structure. So, as
> these two structures are quite different from each other, leads to a large
> change in the rmsd value?
> Thanks and Regards,
> Jac
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