Modified README

This directory contains example data and input files 

as well as utility scripts for the oxDNA/oxDNA2/oxRNA2 

coarse-grained model for DNA and RNA.

coarse-grained model of DNA and RNA.

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/examples/oxDNA2/duplex3:

This is 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.

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 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. 

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).

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

When a large number of atom types is used, this feature allows

quasi-unique base pairing between two individual nucleotides.

The topology is

A   C   G   T   A   C   G   T   A   C   G   T   A

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.

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/examples/oxRNA2/duplex4

This is the duplex2 run with the oxRNA2 force field instead of the oxDNA or 

oxDNA2 force field  and sequence-dependent stacking and hydrogen-bonding 

strengths enabled.

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).

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