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. Author manuscript; available in PMC: 2008 Jul 26.
Published in final edited form as: J Comput Chem. 2005 Dec;26(16):1781–1802. doi: 10.1002/jcc.20289

Table 1.

Key features of NAMD.

Ease of use:

  • Free to download and use.

  • 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.

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.

Basic Simulation:

  • Constant temperature via rescaling, coupling, or Langevin dynamics.

  • Constant pressure via Berendsen or Langevin-Hoover methods.

  • Particle mesh Ewald full electrostatics for periodic systems.

  • Symplectic multiple timestep integration.

  • Rigid water molecules and bonds to hydrogen atoms.

Advanced Simulation:

  • Alchemical and conformational free energy calculations.

  • Automated pair-interaction calculations.

  • Automated pressure profile calculations.

  • Locally enhanced sampling via multiple images.

  • Tcl based scripting and steering forces.

  • Interactive visual steering interface to VMD.