Extra options for computational electrophysiology.

Extra options for computational electrophysiology.

* Added two extra .mdp file parameters 'bulk-offset' that allow to specify
an offset of the swap layers from the compartment midplanes. This is useful
for setups where e.g. a transmembrane protein extends far into at least one
of the compartments. Without an offset, ions would be swapped in the vicinity
of the protein, which is not wanted. Adding an extended water layer comes
at the cost of performance, which is not the case for the offset solution.
* Also made the wording a bit clearer in some places
* Described the new parameters in the PDF manual, updated figure
* replaced usage of sprintf in output routine print_ionlist_legend() by snprintf
* Turned comments describing the variables entering the swapcoords.cpp
  functions into doxygen comments

Change-Id: I2a5314d112384b30f9c910135047cc2441192421