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The apoa.sh model script is for a simple 8-processor job in NAMD. The multiple_images.sh script is to run 8 single-processor jobs in NAMD simultaneously, while the sequential-jobs-separately-submitted.sh script is for submitting a series of jobs in series, as would be done in aimless shooting, for example.
When copying to scratch directories is necessary, it is necessary to do that within the PBS script, since it's not a priori known which compute node will be used. The example script movetoscratch_and_run.sh does this, albeit with some more complicated features that start a new NAMD simulation from an older one.
Small analysis jobs (with VMD, CHARMM, custom C code) should not be run outside the queue system. To run many small jobs, you can write a script that creates bash scripts which then can be qsub'ed. This approach is used in generate_many_child_scripts.sh.
The qnodes_status script gives a summary of the output of the qnodes command (as written, it considers only nodes with the property "group0"). Remove the ":group" argument to qnodes to use this on Quantum2.
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