Constrained Overdamped Langevin Dynamics
The large force constants associated with the stretching of molecular bonds have constrained traditional molecular dynamics to timesteps on the order of 1 fs. By constraining these and other stiff degrees of freedom it is possible to greatly extend the timestep. Older methods for doing this, such as SHAKE, we iterative in nature and therefore expensive. The additional observation that the slow modes of proteins are overdamped and hence first order in time allows the method of N. Gronbech-Jensen and S. Doniach, J. Comp. Chem. 15(9):997-1012 to efficiently perform timesteps on the order of 1 ps.
This method of Constrained Overdamped Langevin Dynamics (COLD) is being incorporated into namd, along with an algorithm for automatically constructing the necessary constraints on stiff degrees of freedom. While not yet sufficiently developed for highly accurate studies, this method will be highly useful for the interactive molecular dynamics planned for MDScope and for simulations in which conformational change is of primary interest.
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