title: A comparative study of molecular dynamics in Cartesian and in internal coordinates: dynamical instability in the latter caused by nonlinearity of the equations of motion.
abstract: The stability of a general molecular dynamics (MD) integration scheme is examined for simulations in generalized (internal plus external) coordinates (GCs). An analytic expression is derived for the local error in energy during each integration time step. This shows that the explicit dependence of the mass-matrix on GCs, which makes the system's Lagrange equations of motion nonlinear, causes MD simulations in GCs to be less stable than those in Cartesian coordinates (CCs). In terms of CCs, the corresponding mass-matrix depends only on atomic masses and thus atomistic motion is subject to the linear Newton equations, which makes the system more stable. Also investigated are two MD methods in GCs that utilize nonzero elements of the vibrational spectroscopic B-matrices. One updates positions and velocities in GCs that are iteratively adjusted so as to conform to the velocity Verlet equivalent in GCs. The other updates positions in GCs and velocities in CCs that are adjusted to satisfy the internal constraints of the new constrained WIGGLE MD scheme. The proposed methods are applied to an isolated n-octane molecule and their performances are compared with those of several CCMD schemes. The simulation results are found to be consistent with the analytic stability analysis. Finally, a method is presented for computing nonzero elements of B-matrices for external rotations without imposing the Casimir-Eckart conditions.
authors.affiliation: Biophysics Research Division and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors.forename: Sang-Ho
authors.initials: SH
authors.lastname: Lee
authors.forename: Kim
authors.initials: K
authors.lastname: Palmo
authors.forename: Samuel
authors.initials: S
authors.lastname: Krimm
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D007700:Kinetics; D008432:Mathematical Computing; D019563:Mechanics; D008968:Molecular Conformation; D009795:Octanes / Q000737:chemistry; D009930:Organic Chemicals / Q000737:chemistry*; D012399:Rotation
chemical_list: D009795:Octanes; D009930:Organic Chemicals; C026728:octane