Coarse-Grained Simulations Of Dna And Rna Systems With Oxdna And Oxrna Models: Tutorial.
Winter Simulation Conference（2023）
摘要
We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and nanotechnology settings. The tutorial is aimed at new users asking "Where should I start if I want to use oxDNA". We assume no prior background in using the model. This tutorial shows basic examples that can get a novice user started with the model, and points the prospective user towards additional reading and online resources depending on which aspect of the model they are interested in pursuing.
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关键词
Nucleic Acid,Simulated DNA,Coarse-grained Model,DNA Nanotechnology,Molecular Dynamics,DNA Strand,Random Generation,Order Parameter,Production Run,Monte Carlo Algorithm,Computer Cluster,Simulation Code,Strand Displacement,Jupyter Notebook,Pseudoknot,Topology Files,Umbrella Sampling,Optional Parameters,DNA Origami,Neighbor List,Group Of Nucleotide,Weighted Histogram Analysis Method,Properties Of RNA,Unbiased Simulations,Large-scale Conformational Changes,Input Files,High-performance Computing,Running,Simulation Parameters,Code Version
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