NAMD

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is file-compatible with AMBER, CHARMM and X-PLOR.

Installed on: Big Ben and pople

Please read the license agreement.

Pople version

  • Executable is named namd2
  • Usage:     Prepare a job script containing commands to:
    • Set up the module command
    • Load the NAMD module: 
      module load namd
    • Use an MPI command like: 
      mpirun -np $PBS_PPN dplace -s1  namd2 prog.namd > prog.log
    • Submit the job script with a qsub command.
  • See the example job.

Big Ben version

  • Version 2.6 is installed in directory /usr/local/packages/namd2/NAMD_2.6-CRAY-XT3. The executable is named namd2.
  • Usage:    Prepare a job script containing commands to:
    • Define these variables: 
      setenv MPICH_PTL_SEND_CREDITS -1
setenv MPICH_MAX_SHORT_MSG_SIZE 8000
setenv MPICH_PTL_UNEX_EVENTS 60000
setenv MPICH_UNEX_BUFFER_SIZE 100M
    • Execute a NAMD program. Be sure to use the correct path according to the version you want. 
      pbsyod /usr/local/packages/namd2/NAMD_2.6-CRAY-XT3/namd2
  • Submit the job script with a qsub command.
  • See the example job.

See also