Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

Yilin Meng; Danial Sabri Dashti; Adrian E. Roitberg

doi:10.1021/ct200153u

Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct200153u ◽

2011 ◽

Vol 7 (9) ◽

pp. 2721-2727 ◽

Cited By ~ 44

Author(s):

Yilin Meng ◽

Danial Sabri Dashti ◽

Adrian E. Roitberg

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Alchemical Free Energy

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Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b03277 ◽

2018 ◽

Vol 122 (41) ◽

pp. 9435-9442 ◽

Cited By ~ 16

Author(s):

Wei Jiang ◽

Jonathan Thirman ◽

Sunhwan Jo ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

Dynamics Method

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A Refined Free Energy Perturbation Hamiltonian Replica Exchange Molecular Dynamics Method for Absolute Binding Affinity Predictions

Biophysical Journal ◽

10.1016/j.bpj.2017.11.3639 ◽

2018 ◽

Vol 114 (3) ◽

pp. 675a

Author(s):

Wei Jiang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Affinity ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

Dynamics Method

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Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

Journal of Chemical Theory and Computation ◽

10.1021/ct1001768 ◽

2010 ◽

Vol 6 (9) ◽

pp. 2559-2565 ◽

Cited By ~ 159

Author(s):

Wei Jiang ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Faculty Opinions recommendation of Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718636459.8572054 ◽

2011 ◽

Author(s):

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Faculty Opinions recommendation of Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.8162956.8572054 ◽

2011 ◽

Author(s):

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Exploring the binding pathways of the 14-3-3ζ protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints

PLoS ONE ◽

10.1371/journal.pone.0180633 ◽

2017 ◽

Vol 12 (7) ◽

pp. e0180633 ◽

Cited By ~ 7

Author(s):

Gabor Nagy ◽

Chris Oostenbrink ◽

Jozef Hritz

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Profiles ◽

Distance Restraints ◽

Free Energy Profiles

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Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach

The Journal of Chemical Physics ◽

10.1063/1.3086832 ◽

2009 ◽

Vol 130 (10) ◽

pp. 104110 ◽

Cited By ~ 34

Author(s):

Jeremy Curuksu ◽

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Nucleic Acids ◽

Replica Exchange ◽

Conformational Sampling ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange

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Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b00047 ◽

2015 ◽

Vol 11 (6) ◽

pp. 2776-2782 ◽

Cited By ~ 50

Author(s):

Gül H. Zerze ◽

Cayla M. Miller ◽

Daniele Granata ◽

Jeetain Mittal

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Energy Surface ◽

Intrinsically Disordered Protein ◽

Replica Exchange ◽

Free Energy Surface ◽

Replica Exchange Molecular Dynamics ◽

Intrinsically Disordered ◽

Disordered Protein

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The investigation of the secondary structure propensities and free-energy landscapes of peptide ligands by replica exchange molecular dynamics simulations

Molecular Simulation ◽

10.1080/08927022.2013.835486 ◽

2013 ◽

Vol 40 (13) ◽

pp. 1015-1025 ◽

Cited By ~ 2

Author(s):

Kadir Demir ◽

Nesrin Kılıç ◽

Fahriye Ceyda Dudak ◽

İsmail Hakkı Boyacı ◽

Fatih Yaşar

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Secondary Structure ◽

Molecular Dynamics Simulations ◽

Peptide Ligands ◽

Replica Exchange ◽

Energy Landscapes ◽

Replica Exchange Molecular Dynamics ◽

Free Energy Landscapes ◽

Dynamics Simulations

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Free Energy Landscape of a DNA−Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics

Nano Letters ◽

10.1021/nl802645d ◽

2009 ◽

Vol 9 (2) ◽

pp. 537-541 ◽

Cited By ~ 135

Author(s):

Robert R. Johnson ◽

Axel Kohlmeyer ◽

A. T. Charlie Johnson ◽

Michael L. Klein

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Carbon Nanotube ◽

Energy Landscape ◽

Replica Exchange ◽

Free Energy Landscape ◽

Replica Exchange Molecular Dynamics

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