Details of Specific Protocols

Details on the theory and behaviour of different Protocols are listed here.

• Relative Hybrid Topology Protocol
  • Overview
  • Scientific Details
    • The Hybrid Topology approach
    • The lambda schedule
    • Simulation overview
      • Simulation Steps
      • Simulation details
    • Getting the free energy estimate
    • Analysis
      • Energetic and replica exchange analysis
      • Structural analysis
  • See Also
  • References
• Absolute Binding Protocol
  • Overview
  • Scientific Details
    • Orientational restraints
    • Partial annihilation scheme
    • The lambda schedule
    • Simulation overview
      • Simulation steps
      • Simulation details
    • Getting the free energy estimate
  • See Also
  • References
• Absolute Solvation Protocol
  • Overview
  • Scientific Details
    • Partial annihilation scheme
    • The lambda schedule
    • Simulation overview
      • Simulation steps
      • Simulation details
    • Getting the free energy estimate
  • See Also
  • References
• Separated Topologies Protocol
  • Overview
  • Scientific Details
    • Orientational restraints
    • Partial annihilation scheme
    • The lambda schedule
    • Simulation overview
      • Simulation steps
      • Simulation details
    • Getting the free energy estimate
  • See Also
  • References
• Plain MD Protocol
  • Overview
  • Scientific Details
    • Simulation Steps and Outputs
    • Performance consideration for gas phase MD simulations
  • See Also
  • References