The Conveyor Belt Umbrella Sampling (CBUS) Scheme: Principle and Application to the Calculation of the Absolute Binding Free Energies of Alkali Cations to Crown Ethers

Journal of Chemical Theory and Computation
David F HahnPhilippe H Hünenberger

Abstract

We recently introduced a method called conveyor belt (CB) thermodynamic integration (TI) for the calculation of alchemical free-energy differences based on molecular dynamics simulations. In the present work, the CBTI approach is generalized to conformational free-energy changes, i.e., to the determination of the potential of mean force (PMF) along a conformational coordinate ξ of interest. The proposed conveyor belt umbrella sampling (CBUS) scheme relies on the parallel simulation of K replicas k = 0,1, ..., K - 1 of the system, with K even. For each replica k, the instantaneous value of ξ is restrained to an anchor value λ k . The latter anchor points are equally spaced along a forward-turn-backward-turn path (i.e., a CB) between two extreme values defining the ξ-range of interest. The rotation of the CB is controlled by a variable Λ (range from 0 to 2π) which evolves dynamically along the simulation. The evolution of Λ results from the forces exerted by the restraining potentials on the anchor points, taken equal and opposite to those they exert on the replicas. Because these forces tend to cancel out along the CB, the dynamics of Λ is essentially diffusive, and the continuous distribution of ξ-values sampled by the replica ...Continue Reading

References

Jan 1, 1986·Annals of the New York Academy of Sciences·H J BerendsenR G Geurtsen
Jul 1, 1987·Journal of Computer-aided Molecular Design·W F van Gunsteren, H J Berendsen
Jun 1, 1994·Journal of Molecular Graphics·J SchlitterP Krüger
Jan 1, 1996·Medicinal Research Reviews·R S BohacekW C Guida
Dec 5, 1988·Physical Review Letters·A M Ferrenberg, R H Swendsen
Dec 23, 1999·Medicinal Research Reviews·N Bodor, P Buchwald
Mar 4, 2000·Biopolymers·M Feig, B M Pettitt
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Dec 17, 2003·Current Opinion in Structural Biology·Dorothee Kern, Erik R P Zuiderweg
Sep 7, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Giovanni CiccottiEric Vanden-Eijnden
Aug 1, 1974·Proceedings of the National Academy of Sciences of the United States of America·M Fixman
Jun 9, 2006·Angewandte Chemie·Wilfred F van GunsterenHaibo B Yu
Jul 11, 2006·The Journal of Chemical Physics·Johannes Kästner, Walter Thiel
Jul 21, 2006·The Journal of Physical Chemistry. B·Alessandro LaioMichele Parrinello
Jul 21, 2006·The Journal of Physical Chemistry. B·Emilio GallicchioRonald M Levy
Jul 21, 2006·The Journal of Physical Chemistry. B·Simone MarsiliVincenzo Schettino
Dec 6, 2006·The Journal of Chemical Physics·Volodymyr BabinCeleste Sagui
Apr 14, 2007·The Journal of Chemical Physics·Tony LelièvreGabriel Stoltz
Apr 10, 2008·The Journal of Chemical Physics·Volodymyr BabinCeleste Sagui
Apr 17, 2008·The Journal of Chemical Physics·Eric DarveAndrew Pohorille
Sep 17, 2008·The Journal of Physical Chemistry. B·Jodi E Basner, Christopher Jarzynski
Dec 3, 2008·The Journal of Chemical Physics·Michael R Shirts, John D Chodera
Dec 3, 2008·The Journal of Chemical Physics·Ben Cooke, Scott C Schmidler
May 8, 2009·Journal of Computational Chemistry·Jennifer L Knight, Charles L Brooks
Dec 25, 2009·Journal of Computational Chemistry·Clara D ChristWilfred F van Gunsteren
Jan 5, 2010·Journal of Chemical Theory and Computation·Edina RostaGerhard Hummer
Jun 12, 2010·The Journal of Physical Chemistry. a·Bruno Martínez-HayaJos Oomens
Dec 21, 2010·Biochimica Et Biophysica Acta·John D McGeaghAdrian J Mulholland
Apr 7, 2011·Journal of Computational Chemistry·Djurre H De JongHelmut Grubmüller
Jun 21, 2011·Journal of Chemical Theory and Computation·Serena DonniniHelmut Grubmüller
Jun 29, 2011·Journal of Computational Chemistry·Hironori KokuboYuko Okamoto
Nov 15, 2011·Journal of Computational Chemistry·Anna-Pitschna E KunzWilfred F van Gunsteren
Nov 24, 2011·Journal of Computational Chemistry·Fangqiang Zhu, Gerhard Hummer
Nov 30, 2011·Journal of Chemical Theory and Computation·Jennifer L Knight, Charles L Brooks
Apr 3, 2012·Physical Review Letters·Soohyung ParkWonpil Im
Apr 17, 2012·The Journal of Chemical Physics·Zhiqiang TanRonald M Levy
Mar 15, 2013·Journal of Chemical Theory and Computation·Soohyung Park, Wonpil Im
Jul 31, 2013·Journal of Molecular Biology·Gabriel J RocklinKen A Dill

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Aug 17, 2020·Journal of Chemical Information and Modeling·Gerhard KönigSereina Riniker

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