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 Solvation Protocol Overview Scientific Details Partial annhilation 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