Elastic molecular dynamics with selfconsistent flexible constraints [1 citations — 1 self]
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Abstract:
A new algorithm for constrained molecular dynamics is proposed. In contrast to the standard approach, the constrained bond-length/bond-angle value is adjusted at each time step so that total energy is minimized with respect to the constrained distances. This can be viewed at as modifying the equilibrium bond-length/bond-angle according to external and centripetal forces. Two approaches are constructed to implement the algorithm. Method I includes all energy terms, but it is neither holonomic nor sympletic. Method II neglects a rotational kinetic energy term, resulting in a more expensive sympletic integrator. Both integrators are reversible and well conserve total energy. Simulation results for collisions between two diatomic molecules, two water molecules, and for a periodic water box are compared and contrasted with SHAKE constrained and free dynamics. These results demonstrate the utility and efficacy of these new methods. I
