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:
/examples/oxDNA3/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/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. 

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/examples/oxDNA3/unique_bp:

This example uses a dsDNA ring of 74 that contains only C-G 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.

The unique base pairs are defined in such a way that no nucleotide is
complementary to the one that is opposite of it in the initial configuration,
but rather complementary to one nucleotide down in 5'-direction. For instance,
nucleotides 1-148 2-147, ... , 73-76, 74-75 are opposite of each other, but the
base pairs are defined as 1-75, 2-148, 3-147 ... 74-76.

Thus, all base pairs are initially broken and anneal during a longer NVT run.  
The associated test compares the average kinetic energy and the hydrogen bonding
energy after annealing.

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

/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.
