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The integration algorithm used in the simulation is based on molecular dynamics. The force field used to describe the various interactions between atoms and groups of atoms in the SAM molecular system is of the TraPPE (transferable potentials for phase equilibria) UA (united atom approach) type. In the TraPPE-UA force field, hydrogen atoms are combined with the carbons they are bonded to, forming a single interaction site, or “pseudoatom”. This is also true for hydrogen bonded to sulfur (head group), where sulfur is left uncharged. The specific details of the functional form and the parametrization of the TraPPE-UA force field are given in [1].

  1. N. Lubna, G. Kamath, J.J. Potoff, N. Rai, and J.I. Siepmann (2005). “Transferable Potentials for Phase Equilibria. 8. United-Atom Description for Thiols, Sulfides, Disulfides, and Thiophene,” J. Phys. Chem. B 109, 24100-24107.