removing get_vx
Bug fix in progress for NPT
added a globalIndex counter to Molecule
fixes for NPT and NVT
Changes to integrate the NVT and NPT ensembles
Many fixes to add extended system
just little things like deleteing unused variables and such.
a few fixes to simError.h also some fixes to Molecule.hpp
Starting work on NPT
Fixes in MPI force calc and in Trappe_Ex parsing.
fixed a bug where the Excludes were not being created properly
fixed the compile time bugs, Source builds and links
fixed a few more bugs.
added the Molecule.cpp file
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