Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins

Josep Lluis Gelpí; Susana G. Kalko; Xavier Barril; Jordi Cirera; Xavier de la Cruz; F. Javier Luque; Modesto Orozco

doi:10.1002/prot.1159

Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.1159 ◽

2001 ◽

Vol 45 (4) ◽

pp. 428-437 ◽

Cited By ~ 52

Author(s):

Josep Lluis Gelpí ◽

Susana G. Kalko ◽

Xavier Barril ◽

Jordi Cirera ◽

Xavier de la Cruz ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Interaction ◽

Interaction Potentials ◽

Dynamics Simulations

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Improving the accuracy of molecular dynamics simulations: parameterisation of interaction potentials for small molecules

10.14264/uql.2018.432 ◽

2018 ◽

Author(s):

Martin Stroet

Keyword(s):

Molecular Dynamics ◽

Small Molecules ◽

Molecular Dynamics Simulations ◽

Interaction Potentials ◽

Dynamics Simulations

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Molecular Dynamics Simulations with Interaction Potentials Including Polarization Development of a Noniterative Method and Application to Water

Molecular Simulation ◽

10.1080/08927029008022130 ◽

1990 ◽

Vol 5 (3-4) ◽

pp. 181-192 ◽

Cited By ~ 99

Author(s):

T. P. Straatsma ◽

J. A. McCammon

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Interaction Potentials ◽

Dynamics Simulations

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Molecular Dynamics Simulations with ab initio Interaction Potentials

Modem Techniques in Computational Chemistry: MOTECC-91 ◽

10.1007/978-94-011-3032-5_21 ◽

1991 ◽

pp. 847-919 ◽

Cited By ~ 2

Author(s):

G. Corongiu ◽

M. Aida ◽

M. F. Pas ◽

E. Clementi

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Interaction Potentials ◽

Dynamics Simulations

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Interaction potentials from periodic density-functional theory calculations: Molecular-dynamics simulations of Au clusters deposited on the TiN (001) surface

The Journal of Chemical Physics ◽

10.1063/1.2140702 ◽

2005 ◽

Vol 123 (24) ◽

pp. 244706 ◽

Cited By ~ 6

Author(s):

N. Cruz Hernández ◽

Javier Fdez. Sanz

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Molecular Dynamics Simulations ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Interaction Potentials ◽

Functional Theory ◽

Au Clusters ◽

Dynamics Simulations

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Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

The Journal of Chemical Physics ◽

10.1063/1.4998149 ◽

2017 ◽

Vol 147 (6) ◽

pp. 064507 ◽

Cited By ~ 3

Author(s):

Yen-Ching Ho ◽

Yi-Siang Wang ◽

Sheng D. Chao

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Intermolecular Interaction ◽

Interaction Potentials ◽

Dynamics Simulations

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Homology modeling and molecular dynamics simulations of Dengue virus NS2B/NS3 protease: insight into molecular interaction

Journal of Molecular Recognition ◽

10.1002/jmr.977 ◽

2009 ◽

pp. n/a-n/a ◽

Cited By ~ 3

Author(s):

Kanin Wichapong ◽

Somsak Pianwanit ◽

Wolfgang Sippl ◽

Sirirat Kokpol

Keyword(s):

Molecular Dynamics ◽

Dengue Virus ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Molecular Interaction ◽

Dynamics Simulations ◽

Ns3 Protease ◽

Insight Into

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Interaction potentials for alumina and molecular dynamics simulations of amorphous and liquid alumina

Journal of Applied Physics ◽

10.1063/1.2901171 ◽

2008 ◽

Vol 103 (8) ◽

pp. 083504 ◽

Cited By ~ 90

Author(s):

Priya Vashishta ◽

Rajiv K. Kalia ◽

Aiichiro Nakano ◽

José Pedro Rino

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Interaction Potentials ◽

Dynamics Simulations ◽

Liquid Alumina

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Prediction of Molecular Interaction between Platelet Glycoprotein Ibα and von Willebrand Factor using Molecular Dynamics Simulations

Journal of Atherosclerosis and Thrombosis ◽

10.5551/jat.32458 ◽

2016 ◽

Vol 23 (4) ◽

pp. 455-464 ◽

Cited By ~ 12

Author(s):

Seiji Shiozaki ◽

Shu Takagi ◽

Shinya Goto

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Von Willebrand Factor ◽

Molecular Interaction ◽

Platelet Glycoprotein ◽

Dynamics Simulations ◽

Von Willebrand ◽

Willebrand Factor

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Molecular dynamics simulations of fluid methane properties usingab initiointermolecular interaction potentials

Journal of Computational Chemistry ◽

10.1002/jcc.21185 ◽

2009 ◽

Vol 30 (12) ◽

pp. 1839-1849 ◽

Cited By ~ 19

Author(s):

Shih-Wei Chao ◽

Arvin Huang-Te Li ◽

Sheng D. Chao

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Interaction Potentials ◽

Dynamics Simulations

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Determination of the accuracy and reliability of molecular dynamics simulations in estimating the melting point of iron: Roles of interaction potentials and initial system configurations

Journal of Molecular Liquids ◽

10.1016/j.molliq.2019.111204 ◽

2019 ◽

Vol 290 ◽

pp. 111204 ◽

Cited By ~ 4

Author(s):

Kejiang Li ◽

Rita Khanna ◽

Jianliang Zhang ◽

Guangyue Li ◽

Hongtao Li ◽

...

Keyword(s):

Molecular Dynamics ◽

Melting Point ◽

Molecular Dynamics Simulations ◽

Initial System ◽

Interaction Potentials ◽

Dynamics Simulations ◽

System Configurations

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