Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

Jason M. Swails; Darrin M. York; Adrian E. Roitberg

doi:10.1021/ct401042b

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

Journal of Chemical Theory and Computation ◽

10.1021/ct401042b ◽

2014 ◽

Vol 10 (3) ◽

pp. 1341-1352 ◽

Cited By ~ 121

Author(s):

Jason M. Swails ◽

Darrin M. York ◽

Adrian E. Roitberg

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Constant Ph ◽

Explicit Solvent

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Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

The Journal of Chemical Physics ◽

10.1063/1.3385470 ◽

2010 ◽

Vol 132 (16) ◽

pp. 165103 ◽

Cited By ~ 50

Author(s):

Alfonso De Simone ◽

Philippe Derreumaux

Keyword(s):

Molecular Dynamics ◽

Molecular Weight ◽

Replica Exchange ◽

Low Molecular Weight ◽

Amyloid Peptides ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent

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Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

Physical Chemistry Chemical Physics ◽

10.1039/c5cp06867c ◽

2016 ◽

Vol 18 (18) ◽

pp. 13052-13065 ◽

Cited By ~ 9

Author(s):

Emanuel K. Peter ◽

Joan-Emma Shea ◽

Igor V. Pivkin

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Protein Folding ◽

Kinetic Monte Carlo ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Accelerated Simulation ◽

Explicit Solvent ◽

Exchange Algorithms

In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC).

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Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations

Biophysical Journal ◽

10.1529/biophysj.107.108019 ◽

2007 ◽

Vol 93 (9) ◽

pp. 3218-3228 ◽

Cited By ~ 40

Author(s):

Srinivasaraghavan Kannan ◽

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Loop Structure ◽

Hairpin Loop ◽

Dna Hairpin ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Dynamics Simulations

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The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent

Journal of Molecular Biology ◽

10.1016/j.jmb.2006.11.015 ◽

2007 ◽

Vol 366 (1) ◽

pp. 275-285 ◽

Cited By ~ 102

Author(s):

Andrij Baumketner ◽

Joan-Emma Shea

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Amyloid Β ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Dynamics Simulations

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Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model

Journal of Chemical Theory and Computation ◽

10.1021/ct900676b ◽

2010 ◽

Vol 6 (4) ◽

pp. 1401-1412 ◽

Cited By ~ 70

Author(s):

Yilin Meng ◽

Adrian E. Roitberg

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Constant Ph

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Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation

The Journal of Chemical Physics ◽

10.1063/1.5027379 ◽

2018 ◽

Vol 149 (7) ◽

pp. 072338 ◽

Cited By ~ 6

Author(s):

Vinícius Wilian D. Cruzeiro ◽

Marcos S. Amaral ◽

Adrian E. Roitberg

Keyword(s):

Molecular Dynamics ◽

Redox Potential ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Constant Ph

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Optimized Explicit-Solvent Replica Exchange Molecular Dynamics from Scratch

The Journal of Physical Chemistry B ◽

10.1021/jp805085y ◽

2008 ◽

Vol 112 (34) ◽

pp. 10386-10387 ◽

Cited By ~ 50

Author(s):

Walter Nadler ◽

Ulrich H. E. Hansmann

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent

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Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.22359 ◽

2008 ◽

Vol 76 (2) ◽

pp. 448-460 ◽

Cited By ~ 46

Author(s):

Srinivasaraghavan Kannan ◽

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Folding Simulations ◽

Dynamics Simulations

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Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

Journal of Chemical Theory and Computation ◽

10.1021/ct200146j ◽

2011 ◽

Vol 7 (8) ◽

pp. 2617-2629 ◽

Cited By ~ 116

Author(s):

Jason A. Wallace ◽

Jana K. Shen

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Constant Ph ◽

Explicit Solvent ◽

Constant Ph Molecular Dynamics

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Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp400530e ◽

2013 ◽

Vol 117 (15) ◽

pp. 4014-4027 ◽

Cited By ~ 45

Author(s):

Niel M. Henriksen ◽

Daniel R. Roe ◽

Thomas E. Cheatham

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Conformational Ensemble ◽

Replica Exchange Molecular Dynamics ◽

Explicit Solvent ◽

Field Assessment ◽

Dynamics Simulations ◽

Ensemble Generation

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