What is NAMD?

NAMD is a parallel, object-oriented molecular dynamics code with Charm++ designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular visualization package VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

Using NAMD

To run any molecular dynamics simulation, you should prepare at least four things:

  • a Protein Data Bank (pdb) file which stores atomic conrrdinates and/or velocities for the system.
  • a Protein Structure File (psf) which stores structural information of the protein, such as various types of bonding interactions.
  • a fore field parameter file which defines bond strengths, equilibrium lengths, etc.
  • a configuration file, in which you specifies all the options that NAMD should adopt in running a simulation. It tells NAMD how the simulation is to be run.

User may copy the demo files and pbs script provided under directory /share1/NAMD/sample. You can modify the pbs script for submitting your MD simulations. 

For single node multicore NAMD : namd2 +p$nc $config

For multinode parallel NAMD charm++ : charmrun ++mpiexec +p$np namd2 $config

For multinode SMP parallel NAMD charm++ : charmrun namd2 ++p $P ++ppn $PPN $config

nc – number of core per node
np – total number of processes/cores
config – config file. (e.g. ubq_ws_eq.conf)
P – total number of PEs (worker threads)
PPN – number of PE per process (Usually PPN=nc-1 as one core per process is used for communication threads)

Additional Information

Official documentation can be obtained from NAMD Website

Related software: VMD (VMD and NAMD are developed by TCBG, University of Illinois)