Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer

Shantenu Jha; Peter V. Coveney; Charles A. Laughton

doi:10.1002/jcc.20300

Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer

Journal of Computational Chemistry ◽

10.1002/jcc.20300 ◽

2005 ◽

Vol 26 (15) ◽

pp. 1617-1627 ◽

Cited By ~ 12

Author(s):

Shantenu Jha ◽

Peter V. Coveney ◽

Charles A. Laughton

Keyword(s):

Nucleic Acid ◽

Force Field ◽

Field Validation ◽

Dna Dodecamer ◽

Force Field Validation

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Direct Comparison of Experimental and Calculated NMR Scalar Coupling Constants for Force Field Validation and Adaptation

Journal of Chemical Theory and Computation ◽

10.1021/ct800241d ◽

2008 ◽

Vol 4 (11) ◽

pp. 1949-1958 ◽

Cited By ~ 9

Author(s):

Franziska F.-F. Schmid ◽

Markus Meuwly

Keyword(s):

Force Field ◽

Coupling Constants ◽

Scalar Coupling ◽

Field Validation ◽

Force Field Validation

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CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Journal of Computational Chemistry ◽

10.1002/jcc.23354 ◽

2013 ◽

Vol 34 (25) ◽

pp. 2135-2145 ◽

Cited By ~ 991

Author(s):

Jing Huang ◽

Alexander D. MacKerell

Keyword(s):

Force Field ◽

Field Validation ◽

Nmr Data ◽

Force Field Validation

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Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.7b11871 ◽

2018 ◽

Vol 122 (21) ◽

pp. 5610-5622 ◽

Cited By ~ 6

Author(s):

Yunhui Ge ◽

Vincent A. Voelz

Keyword(s):

Model Selection ◽

Force Field ◽

Bayesian Approach ◽

Field Validation ◽

Force Field Validation

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UsingJ-Coupling Constants for Force Field Validation: Application to Hepta-alanine

The Journal of Physical Chemistry B ◽

10.1021/jp209597e ◽

2011 ◽

Vol 115 (51) ◽

pp. 15221-15227 ◽

Cited By ~ 20

Author(s):

Panagiota S. Georgoulia ◽

Nicholas M. Glykos

Keyword(s):

Force Field ◽

Coupling Constants ◽

Field Validation ◽

Force Field Validation

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Direct Comparisons of Experimental and Calculated Neutron Structure Factors of Pure Solvents as a Method for Force Field Validation

The Journal of Physical Chemistry B ◽

10.1021/jp076501p ◽

2007 ◽

Vol 111 (45) ◽

pp. 12941-12944 ◽

Cited By ~ 11

Author(s):

Jennie L. Thomas ◽

Douglas J. Tobias ◽

Alexander D. MacKerell

Keyword(s):

Force Field ◽

Field Validation ◽

Structure Factors ◽

Neutron Structure ◽

Force Field Validation

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Explicit treatment of hydrogen bonds in the universal force field: Validation and application for metal-organic frameworks, hydrates, and host-guest complexes

The Journal of Chemical Physics ◽

10.1063/1.4985196 ◽

2017 ◽

Vol 147 (16) ◽

pp. 161705 ◽

Cited By ~ 6

Author(s):

Damien E. Coupry ◽

Matthew A. Addicoat ◽

Thomas Heine

Keyword(s):

Hydrogen Bonds ◽

Force Field ◽

Metal Organic Frameworks ◽

Field Validation ◽

Universal Force Field ◽

Metal Organic ◽

Force Field Validation

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Force Field Validation for Molecular Dynamics Simulations of IRMOF-1 and Other Isoreticular Zinc Carboxylate Coordination Polymers

The Journal of Physical Chemistry C ◽

10.1021/jp076853w ◽

2008 ◽

Vol 112 (15) ◽

pp. 5795-5802 ◽

Cited By ~ 114

Author(s):

Jeffery A. Greathouse ◽

Mark D. Allendorf

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Coordination Polymers ◽

Field Validation ◽

Dynamics Simulations ◽

Force Field Validation

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Simulations of 1-Butyl-3-methylimidazolium Tetrafluoroborate + Acetonitrile Mixtures: Force-Field Validation and Frictional Characteristics

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b04341 ◽

2018 ◽

Vol 122 (29) ◽

pp. 7385-7393 ◽

Cited By ~ 6

Author(s):

Brian Conway ◽

Caleb Uitvlugt ◽

Mark Maroncelli

Keyword(s):

Force Field ◽

Field Validation ◽

Force Field Validation

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Force Field Validation Using Protein Side Chain Prediction

The Journal of Physical Chemistry B ◽

10.1021/jp021564n ◽

2002 ◽

Vol 106 (44) ◽

pp. 11673-11680 ◽

Cited By ~ 127

Author(s):

Matthew P. Jacobson ◽

George A. Kaminski ◽

Richard A. Friesner ◽

Chaya S. Rapp

Keyword(s):

Force Field ◽

Side Chain ◽

Field Validation ◽

Force Field Validation

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The COMPASS force field: Validation for carbon nanoribbons

Physica E Low-dimensional Systems and Nanostructures ◽

10.1016/j.physe.2019.113937 ◽

2020 ◽

Vol 118 ◽

pp. 113937 ◽

Cited By ~ 1

Author(s):

A.V. Savin ◽

M.A. Mazo

Keyword(s):

Force Field ◽

Field Validation ◽

Force Field Validation

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