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