PuReMD-old: back-port run_sim.py from master branch. Update control file...
PuReMD-old: back-port run_sim.py from master branch. Update control file parsing to ignore sPuReMD/PG-PuReMD options.
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PuReMD-old: back-port run_sim.py from master branch. Update control file parsing to ignore sPuReMD/PG-PuReMD options.