lammps/examples/USER/cgdna

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

/examples/duplex3:
This is basically the duplex1 run with sequence-dependent stacking
and hydrogen-bonding strengths enabled and both nucleotide mass and 
moment of inertia set to the value of the standalone implementation 
of oxDNA (M = I = 1). To achieve this, the masses can be set directly 
in the input and data file, whereas the moment of inertia is set via 
the diameter of the ellipsoid in the data file and has a value of 3.16227766.
The change of mass and moment of inertia allows direct comparision of 
e.g. trajectory data, energies or time-dependent observables on a per-timestep 
basis until numerical noise causes deviations at later simulation times. 

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