Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics.

ABSTRACT: We report a serious problem associated with a number of current implementations of Andersen and Langevin dynamics algorithms. When long simulations are run in many segments, it is sometimes possible to have a repeating sequence of pseudorandom numbers enter the calcuation. We show that, if the sequence repeats rapidly, the resulting artifacts can quickly denature biomolecules and are then easily detectable. However, if the sequence repeats less frequently, the artifacts become subtle and easily overlooked. We derive a formula for the underlying cause of artifacts in the case of the Langevin thermostat, and find it vanishes slowly as the inverse square root of the number of time steps per simulation segment. Numerous examples of simulation artifacts are presented, including dissociation of

SUBMITTER: Cerutti DS 

PROVIDER: S-EPMC2632580 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature