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(2) I disabled the block of code in the main CMakeLists file that tries to second guess VC++'s choices for runtime libraries. This was required for me to get CUDA to work in VC 2005 where the compiler always chooses multithreaded libraries. I verified that Brook will still build this way, but I haven't tested it.

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.

Implemented the Ewald summation method in the reference platform. Preliminary cuda prototype is included.

Implemented setting random seed for reference platform, as well as adding it as an option to BrownianIntegrator and AndersenThermostat.

Checked in explicit solvent implementation for Cuda platform (cutoffs, periodic boundary conditions, SETTLE)

Implemented dynamic loading of platforms from DLLs.  Also fixed a lot of compilation errors and warnings under Windows.

Lots of mystical CMake incantations to make Cuda platform compile both static and dynamic libraries correctly

 * capitalization of gpuTypes.h
 * various cmake issues

Changed how kernels get initialized.  StandardMMForceField now has you set the 1-4 interactions explicitly.  CMMotionRemover allows the removal frequency to be set.