NAMD runs on a variety of serial and parallel platforms. While it is trivial to launch a serial program, a parallel program depends on a platform-specific library such as MPI to launch copies of itself on other nodes and to provide access to a high performance network such as Myrinet if one is available.
For typical workstations (Windows, Linux, Mac OS X, or other Unix) with only ethernet networking (100 Megabit or Gigabit), NAMD uses the Charm++ native communications layer and the program charmrun to launch namd2 processes for parallel runs (either exclusively on the local machine with the ++local option or on other hosts as specified by a nodelist file). The namd2 binaries for these platforms can also be run directly (known as standalone mode) for single process runs.
For workstation clusters and other massively parallel machines with special high-performance networking, NAMD uses the system-provided MPI library (with a few exceptions) and standard system tools such as mpirun are used to launch jobs. Since MPI libraries are very often incompatible between versions, you will likely need to recompile NAMD and its underlying Charm++ libraries to use these machines in parallel (the provided non-MPI binaries should still work for serial runs.) The provided charmrun program for these platforms is only a script that attempts to translate charmrun options into mpirun options, but due to the diversity of MPI libraries it often fails to work.