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Atomistic Molecular Dynamics (MD) Simulations. Atomistic MD simulations do not explicitly include the electronic degrees of freedom. Atoms are represented by point particles (atomic centers) interacting through force fields that include a description of non-bonded (e.g., Coulomb and van der Waals) and valence (bonds, bends and dihedrals) interactions. Newtonian equations of motion are solved to yield a time trajectory of atomic positions and velocities, thereby accurately accounting for hydrodynamic effects and yielding static and time autocorrelation functions that enable calculating all structural, thermodynamic and dynamic (transport) properties of interest. Because of the large number of interatomic interactions that must be computed in atomistic MD simulations, this approach is typically limited to systems with 10-100s of thousands of atoms and trajectories over 10-100s of nanoseconds. We have extensive experience in performing state-of-the-art atomistic MD simulations of complex systems as well as in developing and implementing new MD simulation methodologies. Most of these capabilities are incorporated within the molecular simulation package Lucretius.
Few representative publications: 1) D. Bedrov and G.D. Smith, "Thermal conductivity of molecular fluids from molecular dynamics simulations: Application of a new imposed-flux method”, J. Chem. Phys., 2000, 113, 8080-8084. 3) G.D. Smith, D.Y. Yoon, C.G. Wade, D. O'Leary, A. Chen and R.L. Jaffe, "Dynamics of poly(oxyethylene) melts: Comparison of 13C NMR spin-lattice relaxation and dielectric relaxation as determined from simulations and experiments", J. Chem. Phys., 1997, 106, 3798-3805. 4) G.D. Smith, W. Paul, M. Monkenbusch, L. Willner, D. Richter, X.H. Qiu and M.D. Ediger. "Molecular dynamics of a 1,4-polybutadiene melt. comparison of experiment and simulation", Macromolecules, 1999, 32, 8857-8865. 5) C. Ayyagari, D. Bedrov and G.D. Smith, "Structure of atactic polystyrene: A molecular dynamics simulation study", Macromolecules, 2000, 33, 6194-6199. 6) O. Borodin, F. Trouw, D. Bedrov and G.D. Smith, “Dynamics of water in poly(ethylene oxide)/water solutions from molecular dynamics simulations and quasielastic neutron scattering”, J. Phys. Chem. B, 2002, 106, 5184-5193. 7) O. Borodin, D. Bedrov and G.D. Smith, “A molecular dynamics simulation study of dielectric relaxation in aqueous poly(ethylene oxide) solutions”, Macromolecules, 2002, 35, 2410-2412. 8) O. Borodin and G.D. Smith, "Molecular dynamic simulations of poly(ethylene oxide)/LiI melts. I. Structural and conformational properties", Macromolecules, 1998, 31, 8396-8406. 10) McCabe, C.; Bedrov, D.; Smith, G.D.; Cummings, P.T. “Discriminating Between Correlations of Experimental Viscosity Data Using Molecular Dynamics Simulations” Ind. & Eng. Chem. Res. 2001, 40, 473-475 11) Smith, G.D., Bedrov, D., Borodin, O., “A Molecular Dynamics Simulation Study of Hydrogen Bonding in Aqueous Poly(ethylene oxide) Solutions” Phys. Rev. Lett. 2000, 85, 5583-5586 |
When the force fields are parameterized to reproduce high-level QC calculations, MD simulations can provide thermophysical, structural, dynamical, mechanical and transport properties that are in quantitative agreement with experiment. Moreover, the analysis of atomistic MD simulation trajectories provides molecular-level mechanistic insight into experimentally observed structural, thermodynamic, transport and relaxation properties and phenomena that are difficult or impossible to obtain experimentally. MD simulations can also be extended to include explicit proton transfer or chemical reactions.