Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications

The European Physical Journal. E, Soft Matter
Oliver HenrichThomas E Ouldridge

Abstract

During the last decade coarse-grained nucleotide models have emerged that allow us to study 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.

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Citations

Jul 14, 2019·Journal of Computational Chemistry·Antonio SumaLorenzo Rovigatti
Feb 12, 2020·Nucleic Acids Research·Antonio SumaVincenzo Carnevale
Apr 8, 2019·The Journal of Chemical Physics·Michele CaraglioEnrico Carlon
May 21, 2019·Nucleic Acids Research·Tiedong SunLars Nordenskiöld
Jan 25, 2020·The European Physical Journal. E, Soft Matter·Simone Napolitano
Apr 4, 2020·Proceedings of the National Academy of Sciences of the United States of America·Tine CurkRosalind J Allen
Aug 26, 2018·The European Physical Journal. E, Soft Matter·Lorenzo RovigattiJohn Russo
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Oct 3, 2019·Physical Review. E·S K NomidisE Carlon
Feb 24, 2020·The Journal of Chemical Physics·F LanduzziF Ritort
Oct 13, 2020·Nucleic Acids Research·Parth Rakesh DesaiKeir C Neuman
Jan 5, 2021·Royal Society Open Science·Dalibor ChevizovichSlobodan Zdravković
Feb 5, 2021·Journal of Molecular Biology·Andrew I JewettDavid S Goodsell
May 20, 2021·Physical Review. E·Enrico SkoruppaEnrico Carlon

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