Templates for GridEngine queue submission scripts are available for serial or parallel batch NAMD jobs on Farber in /opt/shared/templates/gridengine/namd. Copy and edit the template based on your job by following the usage described in the named-serial.qs or named-parallel.qs, respectively.
/opt/shared/templates/gridengine/namd have changed especially as we learn more about what works best on a particular cluster.