Clarified explanation of new example3

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