Add documentation for using Rosetta with QM packages

[vmullig]

This complements pull request RosettaCommons/main#5662.

Tasks:

• Summary : rosetta_basics/scoring/qm-energy-calculations.md
• Important considerations
  • Molecular system size, rosetta_basics/scoring/qm-energy-calculations.md
  • level of theory, and rosetta_basics/scoring/qm-energy-calculations.md
  • computation time rosetta_basics/scoring/qm-energy-calculations.md
  • Computer memory rosetta_basics/scoring/qm-energy-calculations.md
  • CPU usage (especially in multi-threaded or multi-process contexts) rosetta_basics/scoring/qm-energy-calculations.md
  • Disk usage rosetta_basics/scoring/qm-energy-calculations.md
• Supported third-party quantum chemistry software packages rosetta_basics/scoring/qm-energy-calculations.md
  • GAMESS
    • Installation and setup rosetta_basics/scoring/qm-energy-calculations.md
    • Using GAMESS with Rosetta rosetta_basics/scoring/qm-energy-calculations.md
      • Point energy calculation rosetta_basics/scoring/RosettaQM/GAMESS/GAMESSPointEnergyTutorial1.md
      • Geometry optimization : scripting_documentation/RosettaScripts/multistage/GeometryOptimizationRosettaQM.md
      • Transition states
    • Rosetta-GAMESS bridge code organization
  • Psi4
  • Orca
  • NWChem
• Scoring with GAMESS rosetta_basics/scoring/RosettaQM/GAMESS/GamessSinglePointEnergyCalculation.md
  • Configured from commandline.
  • Configured from RosettaScripts XML.
  • Configured from weights file.
  • Configured from C++ or PyRosetta.
  • Geometry optimization option (and how it differs from GamessQMGeometryOptimizationMover).
  • Fragment molecular orbitals (FMO).
  • Density functional tight-binding (DFTB) semi-empirical method.
    • With FMO
  • Dealing with solvation.
  • Controlling verbosity.
• Geometry optimization with the GamessQMGeometryOptimizationMover
  • Configured from commandline.
  • Configured from RosettaScripts XML.
  • Configured from weights file.
  • Configured from C++ or PyRosetta.
• Constraints.
• Electrostatic Embedding