Determination of thermal intermediate state ensemble of box 5 with restrained molecular dynamics simulations

Liling Zhao; Zhijun Liu; Zanxia Cao; Haiyan Liu; Jihua Wang

doi:10.1016/j.comptc.2011.10.004

Determination of thermal intermediate state ensemble of box 5 with restrained molecular dynamics simulations

Computational and Theoretical Chemistry ◽

10.1016/j.comptc.2011.10.004 ◽

2011 ◽

Vol 978 (1-3) ◽

pp. 152-159 ◽

Cited By ~ 1

Author(s):

Liling Zhao ◽

Zhijun Liu ◽

Zanxia Cao ◽

Haiyan Liu ◽

Jihua Wang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Intermediate State ◽

State Ensemble ◽

Dynamics Simulations ◽

Restrained Molecular Dynamics

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Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2012.01.021 ◽

2012 ◽

Vol 102 (4) ◽

pp. 795-801 ◽

Cited By ~ 39

Author(s):

James Gumbart ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Membrane Insertion ◽

Free Energies ◽

Dynamics Simulations

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Direct determination of the Tolman length from the bulk pressures of liquid drops via molecular dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.3253685 ◽

2009 ◽

Vol 131 (16) ◽

pp. 164705 ◽

Cited By ~ 67

Author(s):

Alan E. van Giessen ◽

Edgar M. Blokhuis

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Direct Determination ◽

Liquid Drops ◽

Tolman Length ◽

Dynamics Simulations

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The Determination of Vibrational Frequencies in H-Bonded Liquids from Molecular Dynamics Simulations

Interactions of Water in Ionic and Nonionic Hydrates ◽

10.1007/978-3-642-72701-6_2 ◽

1987 ◽

pp. 23-26 ◽

Cited By ~ 1

Author(s):

Philippe Bopp

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Vibrational Frequencies ◽

Dynamics Simulations

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Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.9b00062 ◽

2019 ◽

Vol 15 (5) ◽

pp. 3344-3353 ◽

Cited By ~ 13

Author(s):

Junhui Peng ◽

Chuang Yuan ◽

Rongsheng Ma ◽

Zhiyong Zhang

Keyword(s):

Molecular Dynamics ◽

Bayesian Inference ◽

Molecular Dynamics Simulations ◽

Coarse Grained ◽

Atomic Structures ◽

Dynamics Simulations ◽

Restrained Molecular Dynamics

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Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations

Chemical Physics Letters ◽

10.1016/j.cplett.2008.11.044 ◽

2009 ◽

Vol 467 (4-6) ◽

pp. 417-423 ◽

Cited By ~ 21

Author(s):

Yoshio Okiyama ◽

Hirofumi Watanabe ◽

Kaori Fukuzawa ◽

Tatsuya Nakano ◽

Yuji Mochizuki ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Force Fields ◽

Orbital Method ◽

Atomic Charges ◽

Molecular Orbital Method ◽

Classical Molecular Dynamics ◽

Dynamics Simulations

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ChemInform Abstract: Improved Molecular Dynamics Simulations for the Determination of Peptide Structures

ChemInform ◽

10.1002/chin.199349293 ◽

2010 ◽

Vol 24 (49) ◽

pp. no-no

Author(s):

D. F. MIERKE ◽

H. KESSLER

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

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Molecular dynamics simulations applied to the determination of nuclear lifetimes from Doppler-broadened γ-ray line shapes produced in thermal neutron capture reactions

Nuclear Physics A ◽

10.1016/0375-9474(92)90067-t ◽

1992 ◽

Vol 549 (1) ◽

pp. 59-83 ◽

Cited By ~ 21

Author(s):

A. Kuronen ◽

J. Keinonen ◽

H.G. Börner ◽

J. Jolie ◽

S. Ulbig

Keyword(s):

Molecular Dynamics ◽

Thermal Neutron ◽

Molecular Dynamics Simulations ◽

Neutron Capture ◽

Thermal Neutron Capture ◽

Line Shapes ◽

Γ Ray ◽

Dynamics Simulations

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Determination of the charge profile in the KcsA selectivity filter using ab initio calculations and molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/b905991a ◽

2009 ◽

Vol 11 (38) ◽

pp. 8606 ◽

Cited By ~ 5

Author(s):

Sebastian Kraszewski ◽

Céline Boiteux ◽

Christophe Ramseyer ◽

Claude Girardet

Keyword(s):

Molecular Dynamics ◽

Ab Initio Calculations ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Selectivity Filter ◽

Dynamics Simulations

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Determination of thermal properties pure ThO2 using classical molecular dynamics simulations

10.1063/1.4948195 ◽

2016 ◽

Author(s):

Partha S. Ghosh ◽

Karamvir Kaur ◽

K. Ali ◽

A. Arya ◽

G. K. Dey

Keyword(s):

Molecular Dynamics ◽

Thermal Properties ◽

Molecular Dynamics Simulations ◽

Classical Molecular Dynamics ◽

Dynamics Simulations

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Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

ChemPhysChem ◽

10.1002/cphc.200700805 ◽

2008 ◽

Vol 9 (6) ◽

pp. 911-919 ◽

Cited By ~ 23

Author(s):

Saman Alavi ◽

Peter Dornan ◽

Tom K. Woo

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Inclusion Complexes ◽

Guest Molecules ◽

Dynamics Simulations

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