NAMDRun is a package that allows you to call NAMD from within VMD.  It
is designed to hide the details of the NAMD-calling process from the
application as much as possible.  The idea is that you can write a
script that calls NAMD but knows none of the details of the underlying
queuing system.

User commands:

NAMDRun::useDQSDestination <destination_identifier_list>

  Tells NAMDRun to use a particular DQS queue.  See the qsub manpage
  for information on the -q option.


NAMDRun::useDQSResourceList <resource_list>

  Tells NAMDRun to use a particular DQS resource list, e.g.,
  "beowulf.and.short".  See the qsub manpage for information on the -l
  option.


NAMDRun::useNAMDName <namd>

  Tells NAMDRun the name of the namd program; by default this is
  "/usr/local/bin/namd2".  This will be ignored by any queuing system
  (eg namd plugin) that doesn't need it. 


NAMDRun::useQueuingSystem <system>

  Specifies what queuing system to use to run NAMD.
  Possible values: "DQS" "local" "none"


NAMDRun::submitJob <simdir> <namd_opts> <jobname> <confname> <logname>

  Submits a NAMD job to the chosen queuing system.
  All file names are given relative to <simdir> - the directory in
  which NAMD will be run.
    <namd_opts> - special options to pass to NAMD
    <jobname>   - the name of the job
    <confname>  - the name of the configuration file
    <logname>   - the name of the logfile
  submitJob returns a job spec, consisting of {queuetype jobid}.


NAMDRun::abortJob <jobspec>

  Attempts to do a hard kill on the job specified by <jobspec> (as 
  returned by "submitJob"). This proc will use the appropriate 
  system call (e.g.: kill, qdel, etc.) to kill the running sim.
