# QMMM Simulations

  - [Introduction](qmmm_introduction)
  - [Topology and Restart
    Files](QMMM_Restart_and_Topology_Files)
      - [Prerequisites](QMMM_Preparation_Prerequisites)
      - [QM region definition](Qmmm_preparation_basic)
      - [Solvation](Qmmm_preparation_solvation)
      - [Permanent Constraints](Qmmm_preparation_constraints)
  - [Input File](QMMM_Input_File)
      - [QM Parameters](QM_Parameters)
      - [MM Parameters](MM_Parameters)
      - [QM/MM Parameters](QMMM_Parameters)
  - Single Point Calculations
      - [Ground State Energy and Gradient](qmmm_sp_energy)
      - [Excited State Energy](QMMM_Excited_States)
      - [Properties](qmmm_sp_property)
      - [ESP Charge Analysis](QMMM_ESP)
  - Potential Energy Surface Analysis
      - [Optimization](Qmmm_optimization)
      - [ Transition States](QMMM_Transition_States)
      - [Hessians and Frequency](Qmmm_freq)
      - [Reaction Pathway Calculations with
        NEB](Qmmm_NEB_Calculations)
  - [Dynamics](QMMM_Dynamics)
  - [Free Energy Calculations](QMMM_Free_Energy)
  - [Appendix](QMMM_Appendix)
      - [Format of NWChem parameter
        file](QMMM_Appendix#format-of-nwchem-parameter-file)
      - [Conversion from AMBER program parameter files to
        NWChem](QMMM_Appendix#conversion-of-standard-amber-program-parameter-files)
  - [References](QMMM_References)