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

Simulated in project SMARTNANOTOX

Material model

1. Aspect of the user case / system to be simulated:
   1. Aspect of the user case to be simulated and how it forms a part of the total user case:
      Atomistic model of the material surface
   2. Material:
      user input - any material
   3. Geometry:
      a slab of the material, presented in terms of atoms coordinates and bonds between the atoms, periodic in two dimensions (XY plane)
   4. Time lapse:
      thermodynamic limit
   5. Manufacturing process or in-service conditions:
      to be prepared by an external software
   6. Publication:
      

Sorbent model

1. Aspect of the user case / system to be simulated:
   1. Aspect of the user case to be simulated and how it forms a part of the total user case:
      Sorbent molecule and solvent
   2. Material:
      Sorbent molecule: a small organic molecule included into a nanomaterial-biological interaction (binding) simulation
   3. Geometry:
      Rectangular box
   4. Time lapse:
      N/A
   5. Manufacturing process or in-service conditions:
      Prepared set of biomolecules described by the molecular topology files
      Solvent: TIP3P water model
   6. Publication:
      

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