SYMPLECTIC AND TIME REVERSIBLE INTEGRATOR FOR RIGID BODIES

摘要

A symplectic and time-reversible molecular dynamics algorithm is presented for rigid molecules in the quaternion representation. The algorithm is developed on the basis of the Trotter factorisation scheme using a Hamiltonian formalism The structure is similar to that of the velocity Verlet algorithm. Subsequently we describe the coupling of the rigid bodies to a thermostat. The isothermal molecular dynamics is defined by introducing additional pseudo-friction coefficients, according to a generalised Nose-Hoover prescription.