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.