40 lines
1.6 KiB
Plaintext
40 lines
1.6 KiB
Plaintext
This directory contains example data and input files
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and utility scripts for the oxDNA coarse-grained model
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for DNA.
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/examples/duplex1:
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Input, data and log files for a DNA duplex (double-stranded DNA)
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consisiting of 5 base pairs. The duplex contains two strands with
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complementary base pairs. The topology is
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A - C - G - T - A
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T - G - C - A - T
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/examples/duplex2:
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Input, data and log files for a nicked DNA duplex (double-stranded DNA)
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consisiting of 8 base pairs. The duplex contains strands with
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complementary base pairs, but the backbone on one side is not continuous:
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two individual strands on one side form a duplex with a longer single
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strand on the other side. The topology is
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A - C - G - T - A - C - G - T
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T - G - C - A T - G - C - A
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/examples/duplex3:
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This is basically the duplex1 run with sequence-dependent stacking
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and hydrogen-bonding strengths enabled and both nucleotide mass and
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moment of inertia set to the value of the standalone implementation
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of oxDNA (M = I = 1). To achieve this, the masses can be set directly
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in the input and data file, whereas the moment of inertia is set via
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the diameter of the ellipsoid in the data file and has a value of 3.16227766.
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The change of mass and moment of inertia allows direct comparision of
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e.g. trajectory data, energies or time-dependent observables on a per-timestep
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basis until numerical noise causes deviations at later simulation times.
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/util:
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This directory contains a simple python setup tool which creates
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single straight or helical DNA strands, DNA duplexes or arrays of DNA
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duplexes.
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