NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. 

Current NAMD Feature Summary:
1. Software Setup: Free to download and use. (Redistribution prohibited); Precompiled binaries provided for 12 popular platforms; Installed at major NSF supercomputer sites; Portable to virtually any platform with ethernet or MPI; C++ source code and CVS access for modification.
2. Molecule Building: Reads X-PLOR, CHARMM, AMBER, and GROMACS input files; Psfgen tool generates structure and coordinate files for CHARMM force field; Efficient conjugate gradient minimization; Fixed atoms and harmonic restraints; Thermal equilibration via periodic rescaling, reinitialization, or Langevin dynamics.
3. Basic Simulation: Constant temperature via rescaling, coupling, or Langevin dynamics; Constant pressure via Berendsen or Langevin Nose-Hoover methods; Particle mesh Ewald full electrostatics for periodic systems; Symplectic multiple timestep integration; Rigid waters and bonds to hydrogen atoms.
4. Advanced Simulation: Chemical and conformational free energy calculations; Locally enhanced sampling via multiple images; Tcl based scripting and steering forces; Interactive visual steering interface to VMD.
5. Scalable Performance: Based on the Charm++/Converse parallel runtime system; Spatial data decomposition for limited communication pattern; Message driven execution for latency tolerance on commodity networks; Measurement-based load balancing for scaling to hundreds of processors; Largest simulation to date is over 300,000 atoms on 1000 processors.