To do list for basic MD feature

[zhenyuwei99]

mdpy.constraint package

• OPLS
  • mdpy.constraint.OPLSBondConstraint
  • mdpy.constraint.OPLSAngleConstraint
  • mdpy.constraint.OPLSDihedralConstraint
  • mdpy.constraint.OPLSVDWConstraint
• Amber
  • mdpy.constraint.AmberBondConstraint
  • mdpy.constraint.AmberAngleConstraint
  • mdpy.constraint.AmberTorsionConstraint
  • mdpy.constraint.AmberVDWConstraint
• DPD
  • mdpy.constraint.DPDConservativeConstraint
  • mdpy.constraint.DPDDissipativeConstraint
• QM/MM (plan)
  • mdpy.constraint.HartreeForkConstraint
  • mdpy.constraint.DFTConstraint

mdpy.integrator package

• Constraint algorithm (a function take cur_positions and next_positions then return modified_positions)
  • LINCS
  • SETTLE
• Microcanonical ensemble
  • mdpy.integrator.VelocityVerletIntegrator
• Canonical ensemble
  • mdpy.integrator.LangevinIntegrator
  • mdpy.integrator.BerendsenThermostatIntegrator
  • mdpy.integrator.AndersonIntegrator
  • mdpy.integrator.NoseHooverIntegrator
• Isothermal–isobaric ensemble
  • mdpy.integrator.BerendsenBarostatIntegrator
  • mdpy.integrator.HooverIntegrator
• Grandcanonical (plan)

mdpy.recipe package

• mdpy.recipe.OPLSRecipe
• mdpy.recipe.AmberRecipe