Coarse-Grained Simulation of DNA using LAMMPS

Abstract

During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.

arXiv comment16 pages, 13 figures, EPJE topical issue on Advances in Computational Methods for Soft Matter Systems

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Cited by in corpus (12)

• A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
• Length scale dependent elasticity in DNA from coarse-grained and all-atom models
• Topological Linking Determines Elasticity in Limited Valence Networks
• The oxDNA coarse-grained model as a tool to simulate DNA origami
• Overtwisting induces polygonal shapes in bent DNA
• Twist-bend coupling, twist waves and the shape of DNA loops
• Lattice Boltzmann simulations capture the multiscale physics of soft flowing crystals
• Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+
• Nonequilibrium thermodynamics of DNA nanopore unzipping
• Nanostars planarity modulates the elasticity of DNA hydrogels
• 3D polymer simulations of genome organization and transcription across different chromosomes and cell types
• Unzipping of knotted DNA via nanopore translocation