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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. Of course, this approach could be used quite generally.
grid_and_dock.sh is another script illustrating that successive program executions can be included in one simplified shell script. It runs AutoDock and AutoGrid.
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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