Usage

The compilation process will generate three executables in the build/bin folder: oxDNA, DNAnalysis and confGenerator. In what follows, mandatory arguments are enclosed by angular brackets, <...>, while optional arguments are enclosed by square brackets, [...].

Note

All three executables take an input file as their first (mandatory) argument. Example input files can be found in the examples folder, while a more thorough description of the input file options and syntax can be found here.

oxDNA

oxDNA is used to perform the actual simulations.

oxDNA <input_file> [key1=value1] [key2=value2] [...]

The first argument, <input_file>, is the path to the file containing all the simulations’ settings. It can be followed by a list of key=value pairs that overwrite the options found in the input file.

DNAnalysis

DNAnalysis can be used to perform specific analysis on configurations or trajectories generated by oxDNA.

DNAnalysis <input_file> [key1=value1] [key2=value2] [...]

Here the usage is formally identical to oxDNA’s. However, note that the two executables handle some of the options found in the input file differently.

confGenerator

confGenerator can be used to generate simple initial configurations. When used to generate DNA or RNA configurations it is recommended to always set generate_consider_bonded_interactions = true in the input file.

confGenerator <input_file> <box|density> [key1=value1] [key2=value2] [...]

In addition to the input file, confGenerator takes another mandatory argument whose meaning depends on its value. It specifies the simulation box if it is a single number larger than 2 (in which case the simulation box is assumed to be cubic) or if it is an x-separated triplet of numbers that specify the length of the edges of the box (which is assumed to be a cuboid). By contrast, the second mandatory argument is interpreted as a number density if it is smaller than 2.

Warning

This tool generates a configuration by inserting one particle (nucleotide) at a time, provided that its interaction energy does not exceed some predetermined value (which can be set with energy_threshold). It does so by placing each nucleotide randomly, but close to its neighbours, so that it is not too unlikely to end up with a non-overstretched bond. Unfortunately, this procedure makes it extremely unlikely to successfully generate a circular strand.

The following examples generate random initial configurations in a cubic box of size 10, in a cuboid of sizes 10x5x15 and in a cubic box with edge \(L\) such that \(N / L^3 = 0.1\), where \(N\) is the total number of nucleotides specified in the topology file.

confGenerator input 10
confGenerator input 10x5x15
confGenerator input 0.1