NAMD

NAMD is a molecular dynamics program designed for parallel computation. Full and efficient treatment of electrostatic and van der Waals interactions are provided via the Particle Mesh Ewald algorithm. (O(N Log N) NAMD interoperates with CHARMM and X-PLOR as it uses the same force field and includes a rich set of MD features (multiple time stepping, constraints, and dissipatitve dynamics). More information is available from the Theoretical Biophysics Group at the University of Illinois.

• Setup
• Examples
• Documentation and Help

Setup

The modules package controls access to software.

To use the default version of NAMD, include the line:

% module load namd

in your .profile.ext or .login.ext files, or type this command whenever you want to access NAMD for a single session.

The version of namd made available by this module uses both MPI and threads for parallelism. The particle mesh Ewald summation is done using the FFTW library.

After the module is loaded you can run namd using

% namd2 infile > outfile -nodes #n -task_per_node #t

Where #n and #t describe the total number of MPI tasks you've chosen.

mpiexec -n numProcs namd2 input.namd

module swap path path/3.0
module load namd/2.6
mpiexec -n numProcs namd2 input.namd

Examples

Small alpha helix 12 residues (66 atoms)

• Config file
• PDB Structure file
• PSF Structure file
• Execute: namd2 alanin.conf > output

DNA peptide complex 11254 residues, 11040 waters (36573 atoms)

• Config file
• PDB Structure file
• PSF Structure file
• Forcefield files
• Execute: namd2 er-gre.namd > output

Alpha Lipo-protein A 22010 residues, 21458 waters (92224 atoms)

• Config file
• PDB Structure file
• PSF Structure file
• Forcefield files
• Execute: namd2 apoa1.namd > output

Documentation and Help

• NAMD Online Manual