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Clarified explanation of new example3

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Oliver Henrich
2019-07-19 13:29:39 +01:00
parent 0ee0ea109c
commit c2643a519e
1 changed files with 9 additions and 6 deletions
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examples/USER/cgdna/README
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@ -23,12 +23,15 @@ A - C - G - T - A - C - G - T
T - G - C - A T - G - C - A
/examples/duplex3:
This is basically the duplex1 run with both nucleotide mass and moment
of inertia set to the values of the standalone implementation of oxDNA,
which are M=I=1. To achieve this, the masses were set directly, whereas
the diameter of the ellipsoid in the data file was changed to 3.16227766.
This allows direct comparision of e.g. trajectory data or energies on a
per-timestep basis until numerical noise leads eventually to deviations.
This is basically 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.
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.
/util:
This directory contains a simple python setup tool which creates