Scraped the code from PDB Output.  Turns out i still need originalStart and origMolIndices so I can init the binary coords and vels in the right place without having to move that code internal to CheckpointSetup.
Scraped the code from PDB Output.  Turns out i still need originalStart and origMolIndices so I can init the binary coords and vels in the right place without having to move that code internal to CheckpointSetup.

GOMC-WSU/GOMC,GOMC-WSU/GOMC,GOMC-WSU/GOMC,GOMC-WSU/GOMC,GOMC-WSU/GOMC