Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

Journal Article (Journal Article)

We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

Full Text

Duke Authors

Cited Authors

  • Cooke, B; Schmidler, SC

Published Date

  • October 2008

Published In

Volume / Issue

  • 129 / 16

Start / End Page

  • 164112 -

PubMed ID

  • 19045252

Electronic International Standard Serial Number (EISSN)

  • 1089-7690

International Standard Serial Number (ISSN)

  • 0021-9606

Digital Object Identifier (DOI)

  • 10.1063/1.2989802


  • eng