Comparing generalized ensemble methods for sampling of systems with many degrees of freedom
Here, 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 nonequilibrium 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 metenkephalin peptide, in which we evaluate the KullbackLeibler 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 amyloidβ peptide in which we find nonnegligible 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.
 Authors:

^{[1]}
;
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^{[2]}
 Univ. of California, Berkeley, CA (United States)
 Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
 Publication Date:
 Grant/Contract Number:
 AC0205CH11231
 Type:
 Accepted Manuscript
 Journal Name:
 Journal of Chemical Physics
 Additional Journal Information:
 Journal Volume: 145; Journal Issue: 17; Journal ID: ISSN 00219606
 Publisher:
 American Institute of Physics (AIP)
 Research Org:
 Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
 Sponsoring Org:
 USDOE Office of Science (SC)
 Country of Publication:
 United States
 Language:
 English
 Subject:
 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
 OSTI Identifier:
 1413710
Lincoff, James, Sasmal, Sukanya, and HeadGordon, Teresa. Comparing generalized ensemble methods for sampling of systems with many degrees of freedom. United States: N. p.,
Web. doi:10.1063/1.4965439.
Lincoff, James, Sasmal, Sukanya, & HeadGordon, Teresa. Comparing generalized ensemble methods for sampling of systems with many degrees of freedom. United States. doi:10.1063/1.4965439.
Lincoff, James, Sasmal, Sukanya, and HeadGordon, Teresa. 2016.
"Comparing generalized ensemble methods for sampling of systems with many degrees of freedom". United States.
doi:10.1063/1.4965439. https://www.osti.gov/servlets/purl/1413710.
@article{osti_1413710,
title = {Comparing generalized ensemble methods for sampling of systems with many degrees of freedom},
author = {Lincoff, James and Sasmal, Sukanya and HeadGordon, Teresa},
abstractNote = {Here, 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 nonequilibrium 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 metenkephalin peptide, in which we evaluate the KullbackLeibler 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 amyloidβ peptide in which we find nonnegligible 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.},
doi = {10.1063/1.4965439},
journal = {Journal of Chemical Physics},
number = 17,
volume = 145,
place = {United States},
year = {2016},
month = {11}
}