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Blue Waters job submission scripts for NAMD are available in /u/sciteam/jphillip/NAMD_scripts (note that you will not be able to list the contents of /u/sciteam/jphillip but you can access the NAMD_scripts subdirectory).

The scripts for the "latest" version of NAMD (2.14) are runbatch, runbatch_cuda, runbatch_memopt, and runbatch_memopt_cuda.

The runbatch scripts require three arguments:

  • NAMD input file
  • NAMD log file
  • number of nodes (number of cores / 32)
  • processes per node (defaults to 1, choices are 1,2,3,4,31,32)
  • queue (defaults to "normal", other options are "high", "debug", and "short")
  • replica or other args (optional)