NAMD Wiki: NamdAtNCSA
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)