Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying stochastic process to a quasi-stationary distribution. Two requirements for applying parallel replica dynamics are knowledge of the time scale on which the process converges to the quasi-stationary distribution and a mechanism for generating samples from this distribution. By combining a Fleming-Viot particle system with convergence diagnostics to simultaneously identify when the process converges while also generating samples, we can address both points. This variation on the algorithm is illustrated with various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms.
Bibliographical noteFunding Information:
A.B. was supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. G.S. was supported in part by the U.S. Department of Energy Award DE-SC0002085 and the US National Science Foundation PIRE Grant OISE-0967140 . T.L. acknowledges funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007–2013) grant agreement No. 614492 . The authors would also like to thank C. Le Bris, M. Luskin, D. Perez, and A.F. Voter for comments and suggestions throughout the development of this work. The authors would also like to thank the referees for their helpful remarks.
© 2015 Elsevier Inc.
- Accelerated molecular dynamics
- Parallel replica dynamics
- Quasi-stationary distributions