This directory contains example data and input files and utility scripts for the oxDNA coarse-grained model for DNA.

/examples/duplex1: Input, data and log files for a DNA duplex (double-stranded DNA) consisiting of 5 base pairs. The duplex contains two strands with complementary base pairs. The topology is

A - A - A - A - A

T - T - T - T - T

/examples/duplex2: Input, data and log files for a nicked DNA duplex (double-stranded DNA) consisiting of 8 base pairs. The duplex contains strands with complementary base pairs, but the backbone on one side is not continuous: two individual strands on one side form a duplex with a longer single strand on the other side. The topology is

A - A - A - A - A - A - A - A

T - T - T T - T - T - T - T

/util: This directory contains a simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes.