The UWHAM and SWHAM Software Package

Scientific Reports
Bin W ZhangRonald M Levy

Abstract

We introduce the UWHAM (binless weighted histogram analysis method) and SWHAM (stochastic UWHAM) software package that can be used to estimate the density of states and free energy differences based on the data generated by multi-state simulations. The programs used to solve the UWHAM equations are written in the C++ language and operated via the command line interface. In this paper, first we review the theoretical bases of UWHAM, its stochastic solver RE-SWHAM (replica exchange-like SWHAM)and ST-SWHAM (serial tempering-like SWHAM). Then we provide a tutorial with examples that explains how to apply the UWHAM program package to analyze the data generated by different types of multi-state simulations: umbrella sampling, replica exchange, free energy perturbation simulations, etc. The tutorial examples also show that the UWHAM equations can be solved stochastically by applying the RE-SWHAM and ST-SWHAM programs when the data ensemble is large. If the simulations at some states are far from equilibrium, the Stratified RE-SWHAM program can be applied to obtain the equilibrium distribution of the state of interest. All the source codes and the tutorial examples are available from our group's web page: https://ronlevygroup.cst.templ...Continue Reading

References

Jul 21, 2006·The Journal of Physical Chemistry. B·Emilio GallicchioRonald M Levy
Mar 3, 2007·The Journal of Chemical Physics·Bin W ZhangDaniel M Zuckerman
Dec 3, 2008·The Journal of Chemical Physics·Michael R Shirts, John D Chodera
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
Feb 23, 2011·Current Opinion in Structural Biology·Emilio Gallicchio, Ronald M Levy
Mar 5, 2011·Annual Review of Biophysics·Daniel M Zuckerman
Aug 17, 2011·The Journal of Chemical Physics·Jaegil KimJohn E Straub
Nov 24, 2011·Journal of Computational Chemistry·Fangqiang Zhu, Gerhard Hummer
Apr 17, 2012·The Journal of Chemical Physics·Zhiqiang TanRonald M Levy
Jan 1, 2007·Journal of Chemical Theory and Computation·John D ChoderaKen A Dill
Jan 2, 2016·The Journal of Physical Chemistry Letters·Bin W ZhangRonald M Levy
Apr 16, 2016·The Journal of Physical Chemistry. B·Bin W ZhangRonald M Levy
Apr 29, 2016·PLoS Computational Biology·Tatiana MaximovaAmarda Shehu
Jul 28, 2016·Molecular Simulation·Cheng ZhangB Montgomery Pettitt
Sep 14, 2017·Journal of Chemical Theory and Computation·Bin W ZhangRonald M Levy
Apr 11, 2018·The Journal of Physical Chemistry. B·Bin W ZhangRonald M Levy

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Citations

Apr 15, 2021·Journal of Computational Chemistry·Xiangyu JiaYe Mei
May 4, 2021·The Journal of Physical Chemistry Letters·Shima ArastehRonald M Levy
Dec 12, 2020·The Journal of Physical Chemistry. B·Ronald M LevyBin W Zhang
May 30, 2020·The Journal of Physical Chemistry. B·Bin W ZhangRonald M Levy

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Software Mentioned

PLUMED
Stratified RE - SWHAM
BEDAM
GROMACS
WHAM
Stratified RE
Stratified
ST
- SWHAM
RE

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