Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules

摘要

Molecular dynamics integrators are presented for translational and rotational motion of rigid molecules in microcanonical,canonical,and isothermal-isobaric ensembles.The integrators are all time reversible and are also,in some approaches,symplectic for the microcanonical ensembles.They are developed utilizing the quaternion representation on the basis of the Trotter factorization scheme using a Hamiltonian formalism.The structure is similar to that of the velocity Verlet algorithm.Comparison is made with standard integrators in terms of stability and it is found that a larger time step is stable with the new integrators.The canonical and isothermal-isobaric molecular dynamics simulations are defined by using a chain thermostat approach according to generalized Nose-Hoover and Andersen methods.