There are many structural differences between versions 1.X and 2.X of NAMD. Major portions of the code have been completely rewritten, resulting in a program which is significantly faster and uses less memory than earlier versions. This new architecture also provides support for more sophisticated algorithms and is the base for future efficient support of clusters of symmetric multiprocessor workstations. The most noticeable change to the end user is the switch from PVM to the Converse parallel message-passing system. NAMD 2.0 has also been ported to several new platforms.
New features in NAMD 2.0 include periodic boundary conditions, particle-mesh Ewald electrostatic evaluation, Berendsen and Langevin Nosé-Hoover constant pressure simulation methods, fixed atoms, several boundary conditions, triple timestepping, full electrostatic evaluation independent of cycle length, and the ability to do on-the-fly analysis and apply forces to the system via Tcl scripts. The new multiple timestepping parameter nonbondedFreq allows nonbonded interactions to be evaluated less frequently, leaving only bonded interactions to be calculated every timestep. The new spatial partitioning parameters splitPatch and hgroupCutoff have been added due to a change from pairlists to group-based distance checking. The Langevin dynamics and temperature coupling algorithms has been altered to be more suitable for temperature control with small damping coefficients. Finally, NAMD 2.0 can now read CHARMM as well as X-PLOR formatted parameter files.
Several options have been removed in this release. Multiple timestepping is currently limited to impulse methods. Margin checking is performed at every timestep. There are not separate switching and cutoff parameters for van der Waals and electrostatic potentials. Less-used features such as an applied electric field and force DCD files are unimplemented.