This method eliminates the components of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms, allowing a fullElectFrequency of 6 (vs. 4) with a 1 fs timestep without using ``rigidBonds all''. You may use ``rigidBonds water'' but using ``rigidBonds all'' with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen.
The parameters (cellBasisVector[123] and cellOrigin) have not changed, but the basis vectors may now be in any direction.
NAMD now works directly with VMD (http://www.ks.uiuc.edu/Research/vmd/) to allow you to view and interactively steer your simulation. NAMD will wait for VMD to connect on startup.
If for some reason you wish to use the slower DPME implementation of the particle mesh Ewald method add ``useDPME yes''. If you set cellOrigin to something other than (0,0,0) the energy may differ slightly between the old and new implementations. For even better performance get the NAMD source code and compile with FFTW.