Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide

Wenjin Li

doi:10.1063/1.5010408

Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide

The Journal of Chemical Physics ◽

10.1063/1.5010408 ◽

2018 ◽

Vol 148 (8) ◽

pp. 084105

Author(s):

Wenjin Li

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Transition Path ◽

Dynamics Simulations ◽

Alanine Dipeptide

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Reconstructing the Most Probable Folding Transition Path from Replica Exchange Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct400170x ◽

2013 ◽

Vol 9 (8) ◽

pp. 3750-3755 ◽

Cited By ~ 2

Author(s):

Camilo Andres Jimenez-Cruz ◽

Angel E. Garcia

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Transition Path ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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Tackling time-reversibility in transition path sampling molecular dynamics simulations

Molecular Simulation ◽

10.1080/08927022.2011.614241 ◽

2012 ◽

Vol 38 (3) ◽

pp. 211-217

Author(s):

Dirk Zahn

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Path Sampling ◽

Transition Path ◽

Time Reversibility ◽

Transition Path Sampling ◽

Dynamics Simulations

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Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide†

The Journal of Physical Chemistry B ◽

10.1021/jp037422q ◽

2004 ◽

Vol 108 (21) ◽

pp. 6582-6594 ◽

Cited By ~ 129

Author(s):

William C. Swope ◽

Jed W. Pitera ◽

Frank Suits ◽

Mike Pitman ◽

Maria Eleftheriou ◽

...

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Simulations ◽

Folding Kinetics ◽

Dynamics Simulations ◽

Alanine Dipeptide

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Exploring the Mechanisms of Reactions in Solution from Transition Path Sampling Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct0501755 ◽

2005 ◽

Vol 2 (1) ◽

pp. 107-114 ◽

Cited By ~ 15

Author(s):

Dirk Zahn

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Path Sampling ◽

Transition Path ◽

Transition Path Sampling ◽

Dynamics Simulations ◽

Mechanisms Of Reactions

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Direct calculations of vibrational absorption and circular dichroism spectra of alanine dipeptide analog in water: Quantum mechanical/molecular mechanical molecular dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.3243078 ◽

2009 ◽

Vol 131 (13) ◽

pp. 135102 ◽

Cited By ~ 34

Author(s):

Seongeun Yang ◽

Minhaeng Cho

Keyword(s):

Molecular Dynamics ◽

Circular Dichroism ◽

Molecular Dynamics Simulations ◽

Quantum Mechanical ◽

Circular Dichroism Spectra ◽

Vibrational Absorption ◽

Dynamics Simulations ◽

Alanine Dipeptide ◽

Circular Dichroïsm ◽

Direct Calculations

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Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with IR and vibrational circular dichroism spectra

The Journal of Chemical Physics ◽

10.1063/1.2837461 ◽

2008 ◽

Vol 128 (10) ◽

pp. 105106 ◽

Cited By ~ 65

Author(s):

Kijeong Kwac ◽

Kyung-Koo Lee ◽

Jae Bum Han ◽

Kwang-Im Oh ◽

Minhaeng Cho

Keyword(s):

Molecular Dynamics ◽

Circular Dichroism ◽

Molecular Dynamics Simulations ◽

Vibrational Circular Dichroism ◽

Quantum Mechanical ◽

Circular Dichroism Spectra ◽

Dynamics Simulations ◽

Alanine Dipeptide ◽

Circular Dichroïsm

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Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.340030408 ◽

1988 ◽

Vol 3 (4) ◽

pp. 262-265 ◽

Cited By ~ 120

Author(s):

Amil G. Anderson ◽

Jan Hermans

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Probability Map ◽

Dynamics Simulations ◽

Alanine Dipeptide

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Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study

The Journal of Chemical Physics ◽

10.1063/1.2794763 ◽

2007 ◽

Vol 127 (17) ◽

pp. 175105 ◽

Cited By ~ 46

Author(s):

César Augusto F. de Oliveira ◽

Donald Hamelberg ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Accelerated Molecular Dynamics ◽

Explicit Solvent ◽

Kinetic Rates ◽

Dynamics Simulations ◽

Alanine Dipeptide

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Temperature and Pressure Dependence of Alanine Dipeptide Studied by Multibaric−Multithermal Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp712109q ◽

2008 ◽

Vol 112 (38) ◽

pp. 12038-12049 ◽

Cited By ~ 41

Author(s):

Hisashi Okumura ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Pressure Dependence ◽

Temperature And Pressure ◽

Dynamics Simulations ◽

Alanine Dipeptide

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Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Molecular Physics ◽

10.1080/002689700162045 ◽

2000 ◽

Vol 98 (11) ◽

pp. 701-707

Author(s):

Alessandro Sergi, Mauro Ferrario, Francesco Bu

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

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