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- DONE: Allow the parent process in specdesign to be able to run an arbitrary command (specified in the control spec file) that re-evaluates the energy of the solution. Some ideas:
- popen() is a useful function in C.
- the specified command (most conveniently a script) must expect exactly one input string on the command line (the solution/backbone string) and output only one number is to stdout - the new energy.
- Get to the bottom of the apparent MPI slowdown between parent and children processes - a better timing study.
- Implement exclusion list capability (in PDB.pm probably) and allow the possibility of moving self calculations outside of CHARMM. Start by moving vdW such that arbitrary modifications can be easily applied.