Efficient Round-Trip Time Optimization for Replica-Exchange Enveloping Distribution Sampling (RE-EDS)

Journal of Chemical Theory and Computation
Dominik SidlerSereina Riniker

Abstract

Replica-exchange enveloping distribution sampling (RE-EDS) allows the efficient estimation of free-energy differences between multiple end-states from a single molecular dynamics (MD) simulation. In EDS, a reference state is sampled, which can be tuned by two types of parameters, i.e., smoothness parameters(s) and energy offsets, such that all end-states are sufficiently sampled. However, the choice of these parameters is not trivial. Replica exchange (RE) or parallel tempering is a widely applied technique to enhance sampling. By combining EDS with the RE technique, the parameter choice problem could be simplified and the challenge shifted toward an optimal distribution of the replicas in the smoothness-parameter space. The choice of a certain replica distribution can alter the sampling efficiency significantly. In this work, global round-trip time optimization (GRTO) algorithms are tested for the use in RE-EDS simulations. In addition, a local round-trip time optimization (LRTO) algorithm is proposed for systems with slowly adapting environments, where a reliable estimate for the round-trip time is challenging to obtain. The optimization algorithms were applied to RE-EDS simulations of a system of nine small-molecule inhibito...Continue Reading

References

Jul 21, 2004·Journal of Computational Chemistry·Chris OostenbrinkWilfred F van Gunsteren
Dec 17, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Simon TrebstMatthias Troyer
May 13, 2006·The Journal of Chemical Physics·Simon TrebstUlrich H E Hansmann
Feb 13, 2007·Journal of the American Chemical Society·Yng-Gwei Chen, Gerhard Hummer
Mar 16, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Walter Nadler, Ulrich H E Hansmann
May 19, 2007·The Journal of Chemical Physics·Clara D Christ, Wilfred F van Gunsteren
Sep 12, 2007·Journal of Medicinal Chemistry·Christine L GeeJennifer L Martin
Mar 5, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Walter NadlerUlrich H E Hansmann
Dec 25, 2009·Journal of Computational Chemistry·Clara D ChristWilfred F van Gunsteren
Nov 2, 2011·The Journal of Physical Chemistry. B·Sereina RinikerWilfred F van Gunsteren
Sep 28, 2013·Journal of Computer-aided Molecular Design·Shuai LiuDavid L Mobley
Jul 26, 2014·Journal of Chemical Theory and Computation·Juyong LeeBernard R Brooks
Nov 18, 2015·Journal of Chemical Theory and Computation·Juyong LeeBernard R Brooks
Oct 11, 2011·Journal of Chemical Theory and Computation·Andreas P EichenbergerWilfred F van Gunsteren

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Citations

Oct 4, 2018·Journal of Computational Chemistry·Manuela MaurerChris Oostenbrink
Feb 28, 2020·Annual Review of Physical Chemistry·Jan P Unsleber, Markus Reiher
Jan 30, 2021·Journal of Chemical Information and Modeling·Benjamin RiesSereina Riniker
Feb 24, 2020·Current Opinion in Structural Biology·Anita de Ruiter, Chris Oostenbrink
Apr 28, 2018·Journal of Medicinal Chemistry·Doris Alexandra SchuetzGerhard F Ecker
Apr 20, 2018·The Journal of Physical Chemistry. B·Jan Walther Perthold, Chris Oostenbrink
Aug 21, 2021·Journal of Chemical Information and Modeling·Drazen Petrov
Mar 2, 2019·Journal of Chemical Theory and Computation·David F Hahn, Philippe H Hünenberger
Mar 28, 2018·The Journal of Physical Chemistry. B·Justin L MacCallumKari Gaalswyk
Jan 28, 2020·Journal of Chemical Information and Modeling·Kira A ArmacostZoe Cournia
Jun 4, 2020·Journal of Chemical Information and Modeling·Jan Walther PertholdChris Oostenbrink
Aug 17, 2020·Journal of Chemical Information and Modeling·Gerhard KönigSereina Riniker
Sep 4, 2021·Journal of Chemical Theory and Computation·Gerhard KönigSereina Riniker
Jan 4, 2022·Journal of Computer-aided Molecular Design·Benjamin RiesSereina Riniker

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