== Application examples ==

Here, we describe a number of examples of what molecuilder can do with and for your molecular system. 

In the first examples special emphasis is placed on that you are guided through the code thereby as well.

 * ExampleSpatialTranslation - spatial translation of a molecule

In the later examples we just give ideas on how to do things.

 * CreateMicelle - how to create micelle-like structures, embedded in water
 * TremoloWaterExample - we create a box filled with water and simulate with [http://trac.ins.uni-bonn.de/projects/tremolo TREMOLO].
 * DoublingCellContents - we create from a cell filled with atoms a 2x2 grid containing in total 4 times the number of atoms.
 * AlkaneCreation - we create alkanes of arbitrary length from a given one.
 * FormatConversion - we use molecuilder to convert file formats.
 * FragmentingMolecules - how to split a molecule into fragments.
 * CenteringMolecules - how to center molecules with respect to the boundary
 * FragmentationAutomation - how to calculate a molecular system's energy with the BOSSANOVA ansatz and [http://www.mpqc.org MPQC]
 * FittingPotentials - how to fit constant and Morse potentials to a brief water molecule MD simulation