Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation

The Journal of Chemical Physics
Zhiqiang TanRonald M Levy

Abstract

The weighted histogram analysis method (WHAM) including its binless extension has been developed independently in several different contexts, and widely used in chemistry, physics, and statistics, for computing free energies and expectations from multiple ensembles. However, this method, while statistically efficient, is computationally costly or even infeasible when a large number, hundreds or more, of distributions are studied. We develop a locally WHAM (local WHAM) from the perspective of simulations of simulations (SOS), using generalized serial tempering (GST) to resample simulated data from multiple ensembles. The local WHAM equations based on one jump attempt per GST cycle can be solved by optimization algorithms orders of magnitude faster than standard implementations of global WHAM, but yield similarly accurate estimates of free energies to global WHAM estimates. Moreover, we propose an adaptive SOS procedure for solving local WHAM equations stochastically when multiple jump attempts are performed per GST cycle. Such a stochastic procedure can lead to more accurate estimates of equilibrium distributions than local WHAM with one jump attempt per cycle. The proposed methods are broadly applicable when the original data t...Continue Reading

References

Nov 24, 1986·Physical Review Letters·R H Swendsen, J S Wang
Sep 18, 1989·Physical Review Letters·A M Ferrenberg, R H Swendsen
Apr 6, 2001·Physical Review Letters·F Wang, D P Landau
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Jan 22, 2004·Journal of Computational Chemistry·Emilio Gallicchio, Ronald M Levy
Jul 23, 2004·The Journal of Chemical Physics·Donald HamelbergJ Andrew McCammon
Jul 30, 2004·The Journal of Chemical Physics·Ayori Mitsutake, Yuko Okamoto
Sep 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Pu LiuB J Berne
Oct 8, 2005·Journal of Computational Chemistry·Jay L BanksRonald M Levy
Jul 21, 2006·The Journal of Physical Chemistry. B·Emilio GallicchioRonald M Levy
Aug 7, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Sanghyun Park, Vijay S Pande
Sep 20, 2007·Proceedings of the National Academy of Sciences of the United States of America·Weihua ZhengRonald M Levy
Oct 13, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Cheng Zhang, Jianpeng Ma
Nov 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Bin W ZhangDaniel M Zuckerman
Dec 7, 2007·The Journal of Chemical Physics·Jozef Hritz, Chris Oostenbrink
Feb 7, 2008·The Journal of Physical Chemistry. B·Weihua ZhengRonald M Levy
Feb 23, 2008·The Journal of Physical Chemistry. B·Albert C PanBenoît Roux
Dec 3, 2008·The Journal of Chemical Physics·Michael R Shirts, John D Chodera
Dec 3, 2008·The Journal of Chemical Physics·Cheng Zhang, Jianpeng Ma
Jun 11, 2009·The Journal of Chemical Physics·Ayori Mitsutake, Yuko Okamoto
Sep 11, 2009·The Journal of Chemical Physics·Ayori Mitsutake
Nov 10, 2009·The Journal of Chemical Physics·Edina Rosta, Gerhard Hummer
Jan 26, 2010·The Journal of Chemical Physics·Edina Rosta, Gerhard Hummer
Apr 27, 2010·Journal of Chemical Theory and Computation·Emilio GallicchioRonald M Levy
Dec 1, 2010·Journal of Chemical Theory and Computation·Emilio GallicchioRonald M Levy
Nov 24, 2011·Journal of Computational Chemistry·Fangqiang Zhu, Gerhard Hummer
Nov 25, 2011·The Journal of Chemical Physics·John D Chodera, Michael R Shirts
Feb 23, 2012·Journal of Computer-aided Molecular Design·Emilio Gallicchio, Ronald M Levy
Mar 1, 2012·Journal of Chemical Theory and Computation·Mauro LapelosaRonald M Levy
Apr 17, 2012·The Journal of Chemical Physics·Zhiqiang TanRonald M Levy
Oct 23, 2012·Chemical Physics Letters·Daniel B SmithBernard Brooks
Feb 22, 2013·The Journal of Chemical Physics·Phuong H NguyenPhilippe Derreumaux
Aug 21, 2013·The Journal of Chemical Physics·Alexander T HawkDmitrii E Makarov
Sep 6, 2013·Journal of Computational Chemistry·Hironori KokuboYuko Okamoto
Feb 8, 2014·Journal of Computer-aided Molecular Design·Emilio GallicchioRonald M Levy
Nov 18, 2015·Journal of Chemical Theory and Computation·Edina Rosta, Gerhard Hummer
Jul 13, 2010·Journal of Chemical Theory and Computation·Riccardo Chelli
Jan 2, 2016·The Journal of Physical Chemistry Letters·Bin W ZhangRonald M Levy

❮ Previous
Next ❯

Citations

Feb 12, 2017·The Journal of Physical Chemistry. B·Ronald M LevyNobuyuki Matubayasi
Feb 28, 2019·Scientific Reports·Bin W ZhangRonald M Levy
Oct 9, 2019·ELife·Avik BiswasRonald M Levy
Apr 15, 2021·Journal of Computational Chemistry·Xiangyu JiaYe Mei
Apr 11, 2018·The Journal of Physical Chemistry. B·Bin W ZhangRonald M Levy
Jan 29, 2019·Journal of Chemical Theory and Computation·Xinqiang DingCharles L Brooks
Sep 14, 2017·Journal of Chemical Theory and Computation·Bin W ZhangRonald M Levy

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.