Analysis of molecular dynamics simulations trajectories

Prior to v2.1, 3DNA does not provide any direct support for the analysis of molecular dynamics (MD) simulations trajectories of nucleic acid structures. Nevertheless, over the years, I noticed some significant applications of 3DNA in the active MD field; see my blog post (December 6, 2009) titled 3DNA in the PCCP nucleic acid simulations themed issue. In January 2011, I released a set of two Ruby scripts specifically aimed to facilitate the analysis of MD simulations trajectories. Thereafter (as of 3DNA v2.1), I have significantly refined and expanded the Ruby scripts, and consolidated the functionality under one umbrella, x3dna_ensemble with multiple sub-commands (analyze, block_image, extract, and reorient). I believe x3dna_ensemble would make it straightforward to analyze ensembles (NMR or MD simulations trajectories) of nucleic acid structures.

Under this background, I am glad to read recently an article titled Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer in J. Chem. Theory Comput. where 3DNA was used extensively. This work represents a re-visit of the classic Dickerson−Drew B-DNA dodecamer d-[CGCGAATTCGCG]2 using state-of-the-art MD simulations with different ionic conditions and solvation models, and compares the MD trajectories with modern crystallographic and NMR data. Among the author list (Tomas Drsata, Alberto Perez, Modesto Orozco, Alexandre Morozov, Jiri Sponer, and Filip Lankas) are some well-known figures in the MD field of nucleic acid structures.

Reading through the text, I am not sure if the newly available functionality of x3dna_ensemble was used. From the excerpts of the citations given below, however, it seems obvious that 3DNA is now well-accepted by the MD community.

Snapshots taken in 10 ps intervals were analyzed using the 3DNA program.43 From 3DNA outputs, time series of conformational parameters were extracted. These included the intra-base-pair coordinates (buckle, propeller, opening, shear, stretch, and stagger), inter-base-pair or step coordinates (tilt, roll, twist, shift, slide, and rise) as well as groove widths (based on P−P distances), backbone torsions, and sugar puckers.

Contrary to the original work of Lankas et al.,31 the intra-base-pair and step coordinates used here are those defined by 3DNA.43

Here, we apply this model together with the 3DNA definitions of the intra-base-pair and step coordinates.43

However, important differences remain, and non- negligible differences are in fact observed between individual experimental structures also in the central part of DD, even though the intra-base-pair and step coordinates are computed using the same coordinate definitions64 (we consistently use the 3DNA coordinates in this work).



Hi Xiang-jun,

Another older paper which uses 3DNA extensively and which communicates the results in a very appealing manner is the one by Cameron Mura and Andrew McCammon.

Perhaps you’ve already seen it but I’ll leave the link here nonetheless.

This was pre x3dna_ensemble, so, they cooked their own scripts.

Molecular Dynamics of a κB DNA Element: Base Flipping via Cross-strand Intercalative Stacking in a Microsecond-scale Simulation by
Cameron Mura* & J. Andrew McCammon
Nucleic Acids Research (2008), 36(15), 4941–4955.”>mura2008.pdf

Mauricio Esguerra · 2013-01-31 11:26 · #


Hi Mauricio,

Thanks for the info. I may have noticed this paper previously by following 3DNA citations; it is more likely I just read the abstract than the whole paper.

I’ve added the paper to my collection, and will go through it in detail after finishing my work at hand. A quick overview of the article draws my attention to Figure 5 where the authors take advantage of the cross-strand base-overlapping areas from 3DNA:

Cross-strand base overlap areas as a gauge of XSIS. The geometric area of overlap between the planes of nearest-neighbor bases provides a measure of the extent of stacking (e.g. aromatic π–π interactions). Of the four distinct intra- and inter-strand combinations for a base-paired dinucleotide step (i1/i2, j1/j2, i1/j2, j1/i2; see schematic inset), the diagonal terms serve as a particularly sensitive gauge of the degree of cross-strand stacking (i.e. XSIS).

This is the first MD simulation study I am aware of that uses this parameter to quantify base-stacking interactions.


— Xiang-Jun Lu · 2013-01-31 11:57 · #


Dear Xiang-Jun and Mauricio,
It was a pleasant surprise to see these posts. I can confirm that X3DNA played a key role in our analyses of a microsecond-scale DNA trajectory. This was at UCSD back in 2006-7, so a much earlier version of the software. Much of the analysis was achieved via home-grown X3DNA wrappers (an ugly mix of CSH, Matlab, Perl). At the time, I remember thinking the nearest neighbor base overlap was a potentially rather useful (and under-utilized) geometric descriptor for nucleic acid fine structure/local conformation. Many thanks for providing the community with such a powerful and readily usable piece of software!
Best wishes,
Cameron Mura

cameron mura · 2013-06-18 21:16 · #


Hi Cameron,

Thanks for stopping by and for your kind words about 3DNA. Over the years, user feedback has always been a driving force in moving 3DNA forward.

Best regards,


— Xiang-Jun · 2013-06-18 21:32 · #



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