Algorithms for canonical molecular dynamics simulations

Finite-difference algorithms for Nose-Hoover canonical molecular dynamics (NH-MD) are investigated. In general, NH-MD functions excellently, but it is demonstrated that time symmetry is broken in NH-MD algorithms and that this results in irreversible thermostatting, which can destroy the canonical sampling. However, the traditional ‘leapfrog’ algorithm, extended to NH-MD, works almost perfectly and equilibrates correctly, even for a system of a single butane chain, which is found to be very sensitive to numerical approximations. The MD conserves the total momentum—and for a single molecule also the angular momentum. NH-MD can run with or without these conservation constraints, and it is stable with respect to round-off errors, at least for the first 109 time steps for the present system.

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