Modeling chemical reactions in classical molecular dynamics simulations

Molecular Dynamics Simulations of Chemical Reactions for Use in Education

The computational power of computers available to students has increased to the point that it is now feasible to build interactive molecular simulations that can be used in education. In this paper, the simulation engine of an open source program called the Molecular Workbench (1), which can simulate thermodynamics of chemical reactions, is described. While calculating the time evolution of the...

Molecular Dynamics of Chemical Reactions

Molecular beam and spectroscopic techniques allow detailed study of many dynamical properties of single reactive collisions. The chemical scope of these methods is now very wide and includes certain unimolecular and termolecular reactions as well as bimolecular reactions and energy transfer processes. Results for more than 50 families of A + BC — AB + C atom transfer reactions reveal simple imp...

Energy conservation in molecular dynamics simulations of classical systems.

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete "Verlet" algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the o...

Explicit proton transfer in classical molecular dynamics simulations

We present Hydrogen Dynamics (HYDYN), a method that allows explicit proton transfer in classical force field molecular dynamics simulations at thermodynamic equilibrium. HYDYN reproduces the characteristic properties of the excess proton in water, from the special pair dance, to the continuous fluctuation between the limiting Eigen and Zundel complexes, and the water reorientation beyond the fi...

Modeling Nanocomposites for Molecular Dynamics (md) Simulations