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How do I run NAMD2 interactively ?

Please note: The FAQ pages at the HPCVL website are continuously being revised. Some pages might pertain to an older configuration of the system. Please let us know if you encounter problems or inaccuracies, and we will correct the entries.

NAMD requires a number of input files to run. These include:

  • A so-called "configuration file" that declares the initial configuration for a molecular dynamics run, the force field files, number of steps in the simulation, etc.
  • A coordinate file that gives the coordinates of the participating atoms or molecules.
  • A parameter file declaring bond-lengths, angles, dihedrals, non-bonded parameters etc.
  • A force-field file declaring parameters associated with atomic and molecular interactions.

Details about the supported format of these input files can be found in the NAMD User's Guide.

NAMD supports several running modes. In the simplest case, it can be run in serial mode by typing:

namd2 config_file

where config_file is the configuration input file mentioned above. It is recommended to give the configuration file the file extension .namd to enable consistent naming of the output files. These will be generated automatically, and the progress of the program run will be tracked on the screen.

NAMD is also able to run in parallel mode. For our shared-memory systems, it is easiest to run it by specifying the number of threads through the +p option:

namd2 +pN config_file

if N threads are requested.