MODA for Calculations of Binding Free Energies and Potentials of Mean Force

Simulated in project SMARTNANOTOX

1. Post processing:
   1. The processed output is calculated for:
      The raw output is positions of atoms at each trajectory step (Gromacs .xtc or .trr trajectory), value of the collective variable, Gaussian height, force on the collective variable and bias potential (COLVAR , FORCES and HILLS files of Metadynamics). The processed output is the potential of mean force and binding free energy
   2. Methodologies:
      Potential of mean force w(s) is computed by averaging of average force at the given distance of the solute from the surface (s):
      w(s)=-∫_s^s_bulkF(s)ds
      where s_bulk = 1.2 nm is the distance corresponding to bulk solvent where PMF value is accepted to be zero.
      
      The binding free energy is computed by
      ΔG_bind = -k_BT ln(1/δ ∫₀^δ dse^-w(s)/(k_BT),
      where δ is the adsorption layer thickness.
   3. Margin of error: 2 kJ/mol

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