This tutorial show how to run hybrid force matching, i.e. how to use force
matching to only parametrize the non-bonded interactions. For more details
see the paper

"Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane"
Victor Rühle and Christoph Junghans, Macromol.  Theory Simul. 20 (7), 472-477 (2011)
DOI: 10.1002/mats.201100011

In order to run the tutorial, you must first run the reference simulation in the subfolder
md. The atomistic reference run is very short, just to get a guess on the trends. For any
production run you should drastically increase the simulation time and make sure successive
frames are decorrelated. The run script in the md directory  also performas a full 
force-matching run for bonded and non-bonded interactions. 

Then you can run fmatch_intramolecular, which recalculates the forces using gromacs and
then performs a fmatching run for solely the non-bonded contributions.

Things you can do:
- look at the obtained potential *.pot, e.g. A-A.pot from both runs
- analyze the distributions of the atomistic reference run using 
  csg_stat --top topol.tpr --trj fixed_mols.trr --cg hexane.xml --options fmatch.xml 
- setup a coarse-grained run using these obtained potential and compare the 
  distributions with the atomistic reference

