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Title: Sculpting bespoke mountains: Determining free energies with basis expansions

Authors:
 [1];  [2];  [2];  [3];  [2];  [3]
  1. Department of Chemical and Biomolecular Engineering, University of Notre Dame du Lac, Notre Dame, Indiana 46556, USA
  2. Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
  3. Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA, Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1228692
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
The Journal of Chemical Physics
Additional Journal Information:
Journal Name: The Journal of Chemical Physics Journal Volume: 143 Journal Issue: 4; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics
Country of Publication:
United States
Language:
English

Citation Formats

Whitmer, Jonathan K., Fluitt, Aaron M., Antony, Lucas, Qin, Jian, McGovern, Michael, and de Pablo, Juan J. Sculpting bespoke mountains: Determining free energies with basis expansions. United States: N. p., 2015. Web. doi:10.1063/1.4927147.
Whitmer, Jonathan K., Fluitt, Aaron M., Antony, Lucas, Qin, Jian, McGovern, Michael, & de Pablo, Juan J. Sculpting bespoke mountains: Determining free energies with basis expansions. United States. doi:10.1063/1.4927147.
Whitmer, Jonathan K., Fluitt, Aaron M., Antony, Lucas, Qin, Jian, McGovern, Michael, and de Pablo, Juan J. Wed . "Sculpting bespoke mountains: Determining free energies with basis expansions". United States. doi:10.1063/1.4927147.
@article{osti_1228692,
title = {Sculpting bespoke mountains: Determining free energies with basis expansions},
author = {Whitmer, Jonathan K. and Fluitt, Aaron M. and Antony, Lucas and Qin, Jian and McGovern, Michael and de Pablo, Juan J.},
abstractNote = {},
doi = {10.1063/1.4927147},
journal = {The Journal of Chemical Physics},
number = 4,
volume = 143,
place = {United States},
year = {2015},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1063/1.4927147

Citation Metrics:
Cited by: 5 works
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Works referenced in this record:

Multidimensional free-energy calculations using the weighted histogram analysis method
journal, November 1995

  • Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal
  • Journal of Computational Chemistry, Vol. 16, Issue 11
  • DOI: 10.1002/jcc.540161104

Basis Function Sampling: A New Paradigm for Material Property Computation
journal, November 2014


Metadynamics with Adaptive Gaussians
journal, June 2012

  • Branduardi, Davide; Bussi, Giovanni; Parrinello, Michele
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 7
  • DOI: 10.1021/ct3002464

Free energy from constrained molecular dynamics
journal, November 1998

  • Sprik, Michiel; Ciccotti, Giovanni
  • The Journal of Chemical Physics, Vol. 109, Issue 18
  • DOI: 10.1063/1.477419

Efficient Free Energy Calculation of Biomolecules from Diffusion-Biased Molecular Dynamics
journal, October 2012

  • Singh, Sadanand; Chiu, Chi-Cheng; de Pablo, Juan J.
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 11
  • DOI: 10.1021/ct3003755

Metadynamics convergence law in a multidimensional system
journal, May 2010


An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
journal, October 2013

  • Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.
  • The Journal of Chemical Physics, Vol. 139, Issue 14
  • DOI: 10.1063/1.4822042

Potential of mean force between a spherical particle suspended in a nematic liquid crystal and a substrate
journal, October 2002

  • Kim, Evelina B.; Faller, Roland; Yan, Qiliang
  • The Journal of Chemical Physics, Vol. 117, Issue 16
  • DOI: 10.1063/1.1508365

Sculpting bespoke mountains: Determining free energies with basis expansions
journal, July 2015

  • Whitmer, Jonathan K.; Fluitt, Aaron M.; Antony, Lucas
  • The Journal of Chemical Physics, Vol. 143, Issue 4
  • DOI: 10.1063/1.4927147

Accelerating flat-histogram methods for potential of mean force calculations
journal, January 2009

  • Janosi, Lorant; Doxastakis, Manolis
  • The Journal of Chemical Physics, Vol. 131, Issue 5
  • DOI: 10.1063/1.3183165

Nonequilibrium Equality for Free Energy Differences
journal, April 1997


Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods
journal, August 2013

  • Gai, Lili; Vogel, Thomas; Maerzke, Katie A.
  • The Journal of Chemical Physics, Vol. 139, Issue 5
  • DOI: 10.1063/1.4816520

Variational Approach to Enhanced Sampling and Free Energy Calculations
journal, August 2014


GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
journal, February 2013


Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
journal, November 2008


Generic, Hierarchical Framework for Massively Parallel Wang-Landau Sampling
journal, May 2013


Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States
journal, March 2001


PLUMED 2: New feathers for an old bird
journal, February 2014

  • Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide
  • Computer Physics Communications, Vol. 185, Issue 2
  • DOI: 10.1016/j.cpc.2013.09.018

Free Energy Calculations: An Efficient Adaptive Biasing Potential Method
journal, May 2010

  • Dickson, Bradley M.; Legoll, Frédéric; Lelièvre, Tony
  • The Journal of Physical Chemistry B, Vol. 114, Issue 17
  • DOI: 10.1021/jp100926h

Wang-Landau Algorithm for Continuous Models and Joint Density of States
journal, March 2006


Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations
journal, October 2004


α-helix to β-hairpin transition of human amylin monomer
journal, April 2013

  • Singh, Sadanand; Chiu, Chi-cheng; Reddy, Allam S.
  • The Journal of Chemical Physics, Vol. 138, Issue 15
  • DOI: 10.1063/1.4798460

Density of States–Based Molecular Simulations
journal, July 2012


Well-Tempered Metadynamics Converges Asymptotically
journal, June 2014


Potential of mean force between two nanometer-scale particles in a polymer solution
journal, July 2005

  • Doxastakis, M.; Chen, Y. -L.; de Pablo, J. J.
  • The Journal of Chemical Physics, Vol. 123, Issue 3
  • DOI: 10.1063/1.1953575

Single-sweep methods for free energy calculations
journal, May 2008

  • Maragliano, Luca; Vanden-Eijnden, Eric
  • The Journal of Chemical Physics, Vol. 128, Issue 18
  • DOI: 10.1063/1.2907241

New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles
journal, February 1992

  • Lyubartsev, A. P.; Martsinovski, A. A.; Shevkunov, S. V.
  • The Journal of Chemical Physics, Vol. 96, Issue 3
  • DOI: 10.1063/1.462133

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
journal, January 2008


Hyper-parallel tempering Monte Carlo: Application to the Lennard-Jones fluid and the restricted primitive model
journal, December 1999

  • Yan, Qiliang; de Pablo, Juan J.
  • The Journal of Chemical Physics, Vol. 111, Issue 21
  • DOI: 10.1063/1.480282

Flux Tempered Metadynamics
journal, September 2011

  • Singh, Sadanand; Chiu, Chi-cheng; de Pablo, Juan J.
  • Journal of Statistical Physics, Vol. 145, Issue 4
  • DOI: 10.1007/s10955-011-0301-0

Density-of-states Monte Carlo method for simulation of fluids
journal, May 2002

  • Yan, Qiliang; Faller, Roland; de Pablo, Juan J.
  • The Journal of Chemical Physics, Vol. 116, Issue 20
  • DOI: 10.1063/1.1463055

Interactions between spherical colloids mediated by a liquid crystal: A molecular simulation and mesoscale study
journal, July 2004

  • Kim, Evelina B.; Guzmán, Orlando; Grollau, Sylvain
  • The Journal of Chemical Physics, Vol. 121, Issue 4
  • DOI: 10.1063/1.1761054

Isotropic–nematic phase transition in the Lebwohl–Lasher model from density of states simulations
journal, June 2012

  • Shekhar, Raj; Whitmer, Jonathan K.; Malshe, Rohit
  • The Journal of Chemical Physics, Vol. 136, Issue 23
  • DOI: 10.1063/1.4722209

Direct calculation of solid-liquid equilibria from density-of-states Monte Carlo simulations
journal, March 2005

  • Mastny, Ethan A.; de Pablo, Juan J.
  • The Journal of Chemical Physics, Vol. 122, Issue 12
  • DOI: 10.1063/1.1874792

Fast Calculation of the Density of States of a Fluid by Monte Carlo Simulations
journal, January 2003


Computation of free energy profiles with parallel adaptive dynamics
journal, April 2007

  • Lelièvre, Tony; Rousset, Mathias; Stoltz, Gabriel
  • The Journal of Chemical Physics, Vol. 126, Issue 13
  • DOI: 10.1063/1.2711185

Approaching a parameter-free metadynamics
journal, September 2011


An improved Monte Carlo method for direct calculation of the density of states
journal, November 2003

  • Shell, M. Scott; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.
  • The Journal of Chemical Physics, Vol. 119, Issue 18
  • DOI: 10.1063/1.1615966

Constrained reaction coordinate dynamics for the simulation of rare events
journal, April 1989


A Time-Independent Free Energy Estimator for Metadynamics
journal, July 2014

  • Tiwary, Pratyush; Parrinello, Michele
  • The Journal of Physical Chemistry B, Vol. 119, Issue 3
  • DOI: 10.1021/jp504920s

Monte Carlo Simulation Methods for Computing Liquid–Vapor Saturation Properties of Model Systems
journal, May 2013

  • Rane, Kaustubh S.; Murali, Sabharish; Errington, Jeffrey R.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 6
  • DOI: 10.1021/ct400074p

Local elevation: A method for improving the searching properties of molecular dynamics simulation
journal, December 1994

  • Huber, Thomas; Torda, Andrew E.; van Gunsteren, Wilfred F.
  • Journal of Computer-Aided Molecular Design, Vol. 8, Issue 6
  • DOI: 10.1007/BF00124016

Escaping free-energy minima
journal, September 2002

  • Laio, A.; Parrinello, M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
  • DOI: 10.1073/pnas.202427399

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality
journal, August 2003

  • Park, Sanghyun; Khalili-Araghi, Fatemeh; Tajkhorshid, Emad
  • The Journal of Chemical Physics, Vol. 119, Issue 6
  • DOI: 10.1063/1.1590311

Free energy surface of two- and three-dimensional transitions of Au 12 nanoclusters obtained by ab initio metadynamics
journal, May 2010


A boundary correction algorithm for metadynamics in multiple dimensions
journal, August 2013

  • McGovern, Michael; de Pablo, Juan
  • The Journal of Chemical Physics, Vol. 139, Issue 8
  • DOI: 10.1063/1.4818153

A Bias-Exchange Approach to Protein Folding
journal, May 2007

  • Piana, Stefano; Laio, Alessandro
  • The Journal of Physical Chemistry B, Vol. 111, Issue 17
  • DOI: 10.1021/jp067873l

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
journal, February 2015

  • Gil-Ley, Alejandro; Bussi, Giovanni
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 3
  • DOI: 10.1021/ct5009087

Optimization of expanded ensemble methods
journal, October 2008

  • Escobedo, Fernando A.; Martinez-Veracoechea, Francisco J.
  • The Journal of Chemical Physics, Vol. 129, Issue 15
  • DOI: 10.1063/1.2994717

Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation
journal, August 2014

  • Dama, James F.; Rotskoff, Grant; Parrinello, Michele
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 9
  • DOI: 10.1021/ct500441q