The folder mdpar contains the source code of the simulation. The package is coded using Eclipse and the makefiles used are the automatically generated. The subfolder src contains the source code while the subfolder buildscripts contains some scripts that slightly alter the build process to support CUDA. The Release subfolder contains the makefiles to build the simulation. The CUDA contains the makefile to build the simulation with experimental CUDA support. Other folder contain debug and profiling build configuration makefiles.