examples: add patch script to support VMD plugin

Particle trajectories can be visualised with VMD (Visual Molecular
Dynamics) [1] taking advantage of a plugin [2] (under development) for
the H5MD output files. The plugin is still a bit restrictive, the
following patch routine tries to meet these restrictions.

[1] http://www.ks.uiuc.edu/Research/vmd
[2] https://github.com/h5md/VMD-h5mdplugin