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

• NAMD documentation from the University of Illinois at Urbana-Champaign. Includes the User Guide, release notes and information about downloading NAMD to your site.



• Other computational chemistry software installed at PSC.