Clean up TAMC input

[StevenCHowell]

• [ ] Add missing inputs:
  • [ ] ionic conditions of buffer, mentioned in issue 29
  • [ ] B-DNA persistence length (advanced)
  • [ ] B-DNA twist energy prefactor (advanced)
• [ ] Rename double-stranded nucleic acid worm-like chain torsion to B-DNA bead--rod torsion
• [ ] Resolve move direction for B-DNA by either
  • [ ] removing it from the input
  • [ ] adding a parenthetical statement saying "NOT for B-DNA"
• [ ] Remove unused inputs:
  • [ ] number of base pairs per bead
  • [ ] soft rotation averaged over N beads
  • [ ] DCD save frequency
  • [ ] random seed
  • [ ] print debugging information
  • [ ] save file labeling information
  • [ ] keep coarse-grain B-DNA and protein pdb and dcd files
  • [ ] keep duplicate structure when move fails
  • [ ] remove binary pkl cg file
• [ ] Refactor other advanced inputs
  • [ ] low/high Rg cutoff
  • [ ] Z coordinate filter
  • [ ] Z cutoff
  • [ ] plot Rg during run
  • [ ] directed Monte Carlo
  • [ ] check box to use atomic constraints
  • [ ] check box to use non-bonding energies