Skip to main content
eScholarship
Open Access Publications from the University of California

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

  • Author(s): Lincoff, J
  • Sasmal, S
  • Head-Gordon, T
  • et al.

Published Web Location

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097048/
No data is associated with this publication.
Abstract

© 2016 Author(s). We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium (http://www.omnia.md/).

Many UC-authored scholarly publications are freely available on this site because of the UC Academic Senate's Open Access Policy. Let us know how this access is important for you.

Item not freely available? Link broken?
Report a problem accessing this item