Molecular Dynamics of Complex Systems: Non-Hamiltonian, Constrained, Quantum-Classical

Abstract

A theoretically sound and computationally tractable treatment for non-Hamiltonian molecular dynamics is needed for simulations of complex systems. Here, statistical mechanics of non-Hamiltonian systems is derived and it is applied to Nosé-Hoover and related isostats. Then, the most rigorous family of algorithms for integration of equations of motion, Trotter-derived unitary integrators (e.g. SHAKE), are discussed in detail. In the last part we address the generalization of molecular dynamics to treat interacting systems composed of quantum and classical subsystems.