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.
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)
Official documentation can be obtained from NAMD Website
Related software: VMD (VMD and NAMD are developed by TCBG, University of Illinois)