This directory contains example data and input files 
as well as utility scripts for the oxDNA/oxDNA2/oxRNA2 
coarse-grained model of DNA and RNA.

/******************************************************************************/

/examples/oxDNA/duplex1:
/examples/oxDNA2/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     

Note that in this example the stacking and hydrogen-bonding interactions 
are sequence-averaged (cf. keyword 'seqav' in according pair styles).

/******************************************************************************/

/examples/oxDNA/duplex2:
/examples/oxDNA2/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

Note that in this example the stacking and hydrogen-bonding interactions 
are sequence-averaged (cf. keyword 'seqav' in according pair styles).

/******************************************************************************/

/examples/oxDNA2/duplex3:

This example uses the duplex1 with sequence-dependent stacking and
hydrogen-bonding interactions and both nucleotide mass and 
moment of inertia set to the value used in the standalone implementation 
of oxDNA (M = I = 1). 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 comparison of
trajectory data or time-dependent observables on a per-timestep basis. 

As mentioned above, the stacking and hydrogen-bonding interactions 
are sequence-dependent (cf. keyword 'seqdep' in according pair styles).

/******************************************************************************/

/examples/oxDNA2/unique_bp:

This example uses atom types 1-8 to model a 13 base pair duplex.
The nucleotide types are assigned as follows:
A = 1,5; C = 2,6; G = 3,7; T = 4,8

The topology is
A   C   G   T   A   C   G   T   A   C   G   T   A
1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 1 - 2 - 7 - 8 - 1
|   |   |   |   |   |   |   |   |   |   |   |   |
4 - 3 - 2 - 1 - 8 - 7 - 6 - 5 - 4 - 3 - 6 - 5 - 4
T   G   C   A   T   G   C   A   T   G   C   A   T

With a large (32 or 64) number of atom types quasi-unique base pairing 
between two individual nucleotides can be established.

/******************************************************************************/

/examples/oxDNA2/dsring:

This example uses a dsDNA ring of 74 base pairs. The bonds which close the ring 
are (in 3' to 5' direction) between nucleotide 74 and 1 and between nucleotide 
148 and 75, respectively. 

/******************************************************************************/

/examples/oxRNA2/duplex2

This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or 
oxDNA2 force field. Sequence-dependent stacking and hydrogen-bonding 
strengths enabled (cf. keyword 'seqdep' in according pair styles).

/******************************************************************************/

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