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.
  • Calculate average ns/day performance from NAMD log file "TIMING" lines: ns_per_day.py
  • Determine error differences between two NAMD log files' "ENERGY" lines (best for constant energy simulation up to 500 steps, with aligned output between log files): diff_energy.py

Example Simulations