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

Simulated in project SMARTNANOTOX

1. Specific computational modelling metadata:
   1. Numercial solver:
      Verlet algorithm with V-rescale thermostat
      Metadynamics algorithm with collective variable determined as the surface separation distance between the sorbent molecule and surface
   2. Software tool:
      Gromacs 2018 with Plumed 2.5
   3. Time steps: 2 fs, total simulation time ~500 ns
   4. Computational representation:
      1. Physics equation, material relations, material:
         Newton’s equations are discretized in a Verlet scheme. Forces are computed by summation over all atom pairs within the cut-off radius. Long-range electrostatic interactions are treated by the Particle Mesh Ewald (PME)
         Metadynamics with adaptive Gaussians width
   5. Computational boundary conditions:
      Material slab periodic in X and Y direction. Sorbent molecule located outside the slab. Water filling the rest of the simulation box. The whole system is 3D periodic
   6. Additional solver parameters:
      thermostat relaxation time: 1 ps
      real space cutoff: 1 nm
      PME grip spacing: 0.1 nm
      preequilibration time: 2 ns
      fixed height of Gaussians: 0.001 kJ/mol
      Additional potential wall for the sorbent at large distance from the surface:
      U_wall(_s)=k(s-a)⁴
      with the force constant k = 40 kJ/(mol Å⁴) and a = 1.5 nm.
   7. Publication:
      E. G. Brandt and A. P. Lyubartsev “Molecular Dynamics Simulations of Adsorption of Amino Acid Side Chain Analogues and a Titanium Binding Peptide on the TiO2 (100) Surface” J. Phys. Chem. C, 119(32), 18126-18139 (2015) DOI:10.1021/acs.jpcc.5b02670

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