Analysis in MD simulation

Free Energy Calculation in MD Simulation

  • Basic Thermodynamics

  • Implication of Free Energy

  • Statistical Mechanics
    • System can be described using Hamiltonian

    • Different ensemble (fixed system quantities)
      – Canonical ensemble (N,V,T)
      – NPT ensemble

  • Common Free Energy Type
    • Solvation Free Energy / Transfer Free Energy
    • Binding Free energy
    • Confomational Free Energy

  • Calculating Free Energy
    • Experimentally
      – probabilities of finding the system at given states

  • Reversible work of moving the system between two states
    • Computationally
    • Accurate calculations of absolute free energy is nearly impossible due to insufficient sampling in a finite length and time scale simulation.
    • Need different methods to estimate free energy.
    • Common method
      – Thermodynamical integration
      – Free Energy Perturbation (FEP)
      – Umbrella sampling
      – Potential of Mean Force (PMF)
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