A generalized reaction field method for molecular dynamics simulations

1995 ◽  
Vol 102 (13) ◽  
pp. 5451-5459 ◽  
Author(s):  
Ilario G. Tironi ◽  
René Sperb ◽  
Paul E. Smith ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Field Method ◽  
Reaction Field ◽  
Dynamics Simulations

Dielectric properties of liquid phase molecular clusters using the external field method: molecular dynamics study

2014 ◽  
Vol 16 (27) ◽  
pp. 13943-13947 ◽  
Author(s):  
Chathurika D. Abeyrathne ◽  
Malka N. Halgamuge ◽  
Peter M. Farrell ◽  
Efstratios Skafidas
Keyword(s):  
Molecular Dynamics ◽  
Dielectric Constant ◽  
Dielectric Properties ◽  
Electric Fields ◽  
Field Method ◽  
Molecular Clusters ◽  
Reaction Field ◽  
External Electric Fields ◽  
Properties Of Materials ◽  
Dynamics Simulations

A method based on molecular dynamics simulations is presented to determine dielectric properties of materials under external electric fields without prior knowledge of their static dielectric constant, using reaction field approximations.

scholarly journals Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff

2020 ◽  
Vol 22 (45) ◽  
pp. 26419-26437 ◽  
Author(s):  
Alžbeta Kubincová ◽  
Sereina Riniker ◽  
Philippe H. Hünenberger
Keyword(s):  
Molecular Dynamics ◽  
Energy Conservation ◽  
Molecular Dynamics Simulations ◽  
Reaction Field ◽  
Conservative Scheme ◽  
Lennard Jones ◽  
Dynamics Simulations

Shifting and switching schemes are developed to enable strict energy conservation in molecular dynamics simulations relying on reaction-field electrostatic (as well as Lennard-Jones) interactions with an atom-based cutoff truncation.

Advances in biomolecular simulations: methodology and recent applications

2003 ◽  
Vol 36 (3) ◽  
pp. 257-306 ◽  
Author(s):  
Jan Norberg ◽  
Lennart Nilsson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Md Simulations ◽  
Conformational Space ◽  
Multiple Time ◽  
Time Step ◽  
Field Methods ◽  
Reaction Field ◽  
Dynamics Simulations

1. Introduction 2582. Set-up of MD simulations 2602.1 Constant-pressure dynamics 2602.2 Grand-canonical dynamics 2612.3 Boundary conditions 2613. Force fields 2623.1 Proteins 2623.2 Nucleic acids 2653.3 Carbohydrates 2663.4 Phospholipids 2663.5 Polarization 2674. Electrostatics 2674.1 Spherical truncation methods 2684.2 Ewald summation methods 2694.3 Fast multipole (FM) methods 2714.4 Reaction-field methods 2715. Implicit solvation models 2716. Speeding-up the simulation 2736.1 SHAKE and its relatives 2736.2 Multiple time-step algorithms 2746.3 Other algorithms 2757. Conformational space sampling 2757.1 Multiple copy simultaneous search (MCSS) and locally enhanced sampling (LES) 2757.2 Steered or targeted MD 2767.3 Self-guided MD 2767.4 Leaving the standard 3D Cartesian coordinate system: 4D MD and internal coordinate MD 2777.5 Temperature variations 2778. Thermodynamic calculations 2788.1 Lambda (λ) dynamics 2788.2 Extracting thermodynamic information from simulations 2798.3 Non-Boltzmann thermodynamic integration (NBTI) 2798.4 Other methods 2799. QM/MM calculations 28210. MD simulations of protein folding and unfolding 28310.1 High-temperature effects 28410.2 Co-solvent and polarization effects 28810.3 External force effects 28811. On the horizon 29112. Acknowledgements 29213. References 292Molecular dynamics simulations are widely used today to tackle problems in biochemistry and molecular biology. In the 25 years since the first simulation of a protein computers have become faster by many orders of magnitude, algorithms and force fields have been improved, and simulations can now be applied to very large systems, such as protein–nucleic acid complexes and multimeric proteins in aqueous solution. In this review we give a general background about molecular dynamics simulations, and then focus on some recent technical advances, with applications to biologically relevant problems.

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