Re: [AMBER] some doubts about simulation analysis

From: Jiri Sponer <>
Date: Sat, 27 Jun 2015 10:28:59 +0200 (MEST)

I would suggest 50 ns is not sufficient to fully converge B-DNA.
I addition, in B-DNA, the most interesting thing usually is
the sequence-dependent variability, i.e. details.
Though it always depends on your research goal which is not clear
from your email.
RMSd is essentially useless, one of the least informative things.
Few recent papers (not a full overview):

mu ABC: a systematic microsecond molecular dynamics study of
tetranucleotide sequence effects in B-DNA
By: Pasi, Marco; Maddocks, John H.; Beveridge, David; et al.
NUCLEIC ACIDS RESEARCH Volume: 42 Issue: 19 Pages: 12272-12283
Published: OCT 29 2014

Convergence and reproducibility in molecular dynamics simulations of the
By: Galindo-Murillo, Rodrigo; Roe, Daniel R.; Cheatham, Thomas E., III
Special Issue: SI Pages: 1041-1058 Published: MAY 2015

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA
By: Zgarbova, Marie; Otyepka, Michal; Sponer, Jiri; et al.
3177-3189 Published: AUG 2014

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta
Torsion Force Field Parameters
By: Zgarbova, Marie; Javier Luque, F.; Sponer, Jiri; et al.
2339-2354 Published: MAY 2013

Mechanical properties of symmetric and asymmetric DNA A-tracts:
implications for looping and nucleosome positioning
By: Drsata, Tomas; Spackova, Nada; Jurecka, Petr; et al.
NUCLEIC ACIDS RESEARCH Volume: 42 Issue: 11 Pages: 7383-7394
Published: 2014

Analyzing ion distributions around DNA: sequence-dependence of potassium
ion distributions from microsecond molecular dynamics
By: Pasi, Marco; Maddocks, John H.; Lavery, Richard
NUCLEIC ACIDS RESEARCH Volume: 43 Issue: 4 Pages: 2412-2423
Published: FEB 27 2015

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in
By: Dans, Pablo Daniel; Faustino, Ignacio; Battistini, Federica; et al.
NUCLEIC ACIDS RESEARCH Volume: 42 Issue: 18 Pages: 11304-11320
Published: OCT 13 2014

etc. etc.

I would suggest you need to extensively read literature, answers to all
your questions are there, and many times.

One of your questions is difficult, and it is stacking.
Unfortunately, we do not see a tool, for a variety of reasons,
to subtract stacking free energies from simulations.
A key problem is the unknown single-strand reference state.
You can monitor MM stacking interaction energy along the
trajectory, but there is no guarantee
it correlates with free energies of duplex formation.
We explained the reason for that in some studies.

Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum
Chemistry, Molecular Mechanics, and Experiment
By: Sponer, Jiri; Sponer, Judit E.; Mladek, Arnost; et al.
BIOPOLYMERS Volume: 99 Issue: 12 Special Issue: SI Pages: 978-988
Published: DEC 2013

Comment on "Computational Model for Predicting Experimental RNA and DNA
Nearest-Neighbor Free Energy Rankings"
By: Sponer, Jiri; Morgado, Claudio A.; Svozil, Daniel
JOURNAL OF PHYSICAL CHEMISTRY B Volume: 116 Issue: 28 Pages:
8331-8332 Published: JUL 19 2012

Best wishes Jiri

Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133

On Sat, 27 Jun 2015, Mary Varughese wrote:

> Date: Sat, 27 Jun 2015 13:23:28 +0530
> From: Mary Varughese <>
> Reply-To: AMBER Mailing List <>
> To: AMBER Mailing List <>
> Subject: [AMBER] some doubts about simulation analysis
> Sir,
> I need to clear some concerns;
> Is a 50ns simulation a short time scale with respect to DNA ( containing
> modified bases)? is there really any need to run simulations over one micro
> second?
> When i do a 50 ns simulation how can i tell the reason for that time scale.
> The backbone rmsd plot shows somewhat stable trajectory. is not it enough.
> How can i convince people?
> could i give a measurement of the stability of the duplex or trajectory? Is
> there any such analysis method to do that? stable backbone rmsd, all
> hydrogen bonds retained throughout, backbone dihedrals and puckering within
> the range though broadly distributed is not that enough evidence?
> When there is enhancement of stacking, Could by any means, can i show the
> enhanced stacking. Is there any method. quantitative other than visually?
> in AMBER? any energy analysis methods?
> On calculating helical parameters on a representative structure, should i
> give the parameters for each base-pair/step? is not average value enough. ?
> the trajectory obtained through MD , its usual that all the values not
> stick to the standard text book values but the average falls in the
> required range. Isnt? Some reduction in helical twist upon simulation is
> always observed isnt.(so it would deviate from nmr data isnt?)
> It wil be really helpful to have some suggestions.
> Thanking you
> Mary Varughese
> _______________________________________________
> AMBER mailing list

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Received on Sat Jun 27 2015 - 01:30:02 PDT
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