Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method

Replica Exchange ◽

Exchange Method ◽

Efficient Sampling ◽

Dynamics Simulations ◽

Replica Exchange Method

Replica exchange reactive molecular dynamics simulations of initial reactions in zeolite synthesis

Physical Chemistry Chemical Physics ◽

10.1039/c5cp03063c ◽

2015 ◽

Vol 17 (38) ◽

pp. 25421-25428 ◽

Cited By ~ 8

Author(s):

Zhifeng Jing ◽

Liang Xin ◽

Huai Sun

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Zeolite Synthesis ◽

Exchange Method ◽

Reactive Molecular Dynamics ◽

Dynamics Simulations ◽

Replica Exchange Method

Silicate oligomerization reactions at realistic temperature were probed by direct simulations using the replica exchange method.

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24695 ◽

2014 ◽

Vol 82 (12) ◽

pp. 3410-3419 ◽

Cited By ~ 8

Author(s):

Katja Ostermeir ◽

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Network Analysis ◽

Replica Exchange ◽

Elastic Network ◽

Dynamics Simulations ◽

Domain Motions

On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction

The Journal of Chemical Physics ◽

10.1063/1.1472510 ◽

2002 ◽

Vol 116 (20) ◽

pp. 9058-9067 ◽

Cited By ~ 515

Author(s):

Hiroaki Fukunishi ◽

Osamu Watanabe ◽

Shoji Takada

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Replica Exchange ◽

Biomolecular Systems ◽

Exchange Method ◽

Efficient Sampling ◽

Replica Exchange Method

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo models

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24068 ◽

2012 ◽

Vol 80 (7) ◽

pp. 1744-1754 ◽

Cited By ~ 10

Author(s):

Hao Fan ◽

Xavier Periole ◽

Alan E. Mark

Keyword(s):

Molecular Dynamics ◽

De Novo ◽

Replica Exchange ◽

Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange

Journal of Chemical Theory and Computation ◽

10.1021/ct7002258 ◽

2008 ◽

Vol 4 (3) ◽

pp. 477-487 ◽

Cited By ~ 32

Author(s):

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Network Analysis ◽

Replica Exchange ◽

Elastic Network ◽

Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

PLoS ONE ◽

10.1371/journal.pone.0060995 ◽

2013 ◽

Vol 8 (4) ◽

pp. e60995 ◽

Cited By ~ 15

Author(s):

Nanyu Han ◽

Yuguang Mu

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins

Journal of Computational Chemistry ◽

10.1002/jcc.25070 ◽

2017 ◽

Vol 38 (31) ◽

pp. 2730-2746 ◽

Cited By ~ 3

Author(s):

Agnieszka S. Karczyńska ◽

Cezary Czaplewski ◽

Paweł Krupa ◽

Magdalena A. Mozolewska ◽

Keehyoung Joo ◽

...

Keyword(s):

Molecular Dynamics ◽

Coarse Grained ◽

Replica Exchange ◽

Model Quality ◽

Dynamics Simulations ◽

Coarse Grained Molecular Dynamics

Faculty Opinions recommendation of Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations.

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

10.3410/f.1048003.498039 ◽

2006 ◽

Author(s):

D Peter Tieleman

Keyword(s):

Molecular Dynamics ◽

Replica Exchange ◽

K Channel ◽

X Ray ◽

X Ray Crystallography ◽

Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

The Journal of Physical Chemistry B ◽

10.1021/jp802469g ◽

2008 ◽

Vol 112 (47) ◽

pp. 15064-15073 ◽

Cited By ~ 33

Author(s):

In-Chul Yeh ◽

Michael S. Lee ◽

Mark A. Olson

Keyword(s):

Molecular Dynamics ◽

Heat Capacity ◽

Replica Exchange ◽

Implicit Solvent ◽

Solvent Models ◽

Dynamics Simulations ◽

Implicit Solvent Models

3P314 Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulations(30.Miscellaneous topics,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.53.s264_1 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S264

Author(s):

Shigehisa Watanabe ◽

Suyong Re ◽

Eiro Muneyuki ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Conformational Analysis ◽

Annual Meeting ◽

Replica Exchange ◽

Biophysical Society ◽