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NAMD Utilities

Related Packages

• VMD (with its plugins and script library) is closely tied to NAMD and is used for:
  • visualizing the initial structure and trajectory
  • assembling biomolecular aggregates
  • solvating the system in a membrane and/or water
  • building the molecular structure (PSF file)
  • visualizing and analyzing the trajectory
• Tcl is used within NAMD and VMD to provide scripting capabilities.
• FFTW 2.1.5 may be compiled into NAMD for better PME performance.
• CHARMM may be useful for setup and analysis.
• The CHARMM parameters are available for use with NAMD.
• Find CHARMM docs and forums at www.charmm.org.
• The Cornell et al. (AMBER) parameters are available in CHARMM format for use with NAMD.
• The OPLS parameters are available in CHARMM format for use with NAMD. OPLS requires the vdwGeometricSigma option, see NamdAndOPLS on the NamdWiki.
• Alchemify by Jérôme Hénin prepares files for alchemical free energy calculations.
• namd_ti.pl Perl script for analysis of output files from thermodynamic integration method in Alchemical Free Energy Module of NAMD2.

Useful Scripts

• VMD plugins and script library
• The namdplot csh script works with Grace to plot energies, etc. (This older version uses XMGR.)
• VMD's new namdplot plugin works on Windows and has both text and graphical interfaces.
• namdstats prints average energies, etc.
• namdpstats print average on pressures for runs with outputPressure enabled.
• namddat is a hack of namdplot to write data to a file
• This front-end simplifies running NAMD and even works with our DQS setup.
• These MATLAB scripts read and write DCD trajectory files.
• Andriy Anishkin's scripts
• Supercomputer batch job submission scripts:
  • runbatch_anvil - Python script for submitting Slurm jobs on Purdue ITaP Anvil supercomputer CPU subsystem.

Example Simulations

• Full examples, including structure building, are in the tutorials
  
  
• ApoA1 benchmark (92,224 atoms, periodic, PME)
  config, directory, 2.8M .tar.gz, 2.7M .zip
  ApoA1 has been the standard NAMD cross-platform benchmark for years.
  
  
• ATPase benchmark (327,506 atoms, periodic, PME)
  config, directory, 27M .tar.gz, 27M .zip
  
  
• STMV (virus) benchmark (1,066,628 atoms, periodic, PME)
  config, directory, 27M .tar.gz, 27M .zip
  STMV is useful for demonstrating scaling to thousands of processors.
  
  
• 20STMV and 210STMV benchmarks from SC14 paper
  directory, 2.5K .tar.gz,
  
  
• tiny benchmark (507 atoms, periodic, PME)
  config, directory, 33K .tar.gz, 32K .zip
  This single-patch benchmark runs at about 14 ms per step and is representative of the workload of a single processor in a larger simulation. For increased parallelism (up to 8 patches) add one or more of "twoAwayX yes", "twoAwayY yes", and "twoAwayZ yes" to the config file.
  
  
• RAMD 5 examples ( 16M .tar.gz, 16M .zip)
  
  
• RAMD 4.1 examples (5.5M .tar.gz, 5.5M .zip)
  
  
• Interactive BPTI (882 atoms, small) (README, config, directory, 56K .tar.gz, 54K .zip)
• ER-GRE benchmark (36573 atoms, spherical) (config, directory, 1.1M .tar.gz, 1.0M .zip)
• decalanin (66 atoms, tiny, ancient) (config, directory, .tar.gz, .zip)
• Tcl forces (decalanin) (config, directory, .tar.gz, .zip)