Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies

Lopes, Pedro E. M.; Harder, Edward; Roux, Benoı̂t; MacKerell, Alexander D.

doi:10.1007/978-1-4020-9956-4_9

Cited by 11 publications

(13 citation statements)

References 211 publications

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“…37 Charge redistribution in response to the change in the local electrostatic field is approximated by updating self-consistently the positions of these auxiliary particles to their local energy minima for any given configuration of the atoms in the system, thereby taking into account the permanent electric field due to the fixed charges and the contribution of the induced dipoles to the electric field. 38 In the context of MD simulations, this self-consistent field (SCF) approach is substituted with an extended Lagrangian integration, which treats electronic degrees of freedom as additional classical dynamic variables. 39–40 This allows for computational efficiency required for long-time MD simulations.…”

Section: Methodsmentioning

confidence: 99%

Competition among Li⁺, Na⁺, K⁺, and Rb⁺ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

2015

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In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions.

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Section: Methodsmentioning

confidence: 99%

Competition among Li⁺, Na⁺, K⁺, and Rb⁺ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

2015

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“…26,27,17,28 These are the fluctuating charge model, the polarizable dipole (a.k.a. induced dipole) model, and the classical Drude oscillator (a.k.a.…”

Section: Potential Energy Functionsmentioning

confidence: 99%

“…Additional background information on both additive and polarizable force fields may be found in a number of recently published reviews. 14,15,16,17 …”

Section: Introductionmentioning

confidence: 99%

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

Vanommeslaeghe

MacKerell

2015

Biochimica et Biophysica Acta (BBA) - General Subjects

266

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Background Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. Scope of Review As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular bimolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields’ parametrization philosophy and methodology. Major Conclusions Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1 microsecond on proteins, DNA, lipids and carbohydrates. General Significance Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers a model that is an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics.

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“…While the present review begins with a brief update on the status of additive protein FFs, here we primarily focus on the latest developments in the inclusion of electronic polarizability into protein FFs. Emphasis is placed on the CHARMM Drude polarizable FF and the polarizable AMOEBA FF, and we direct interested readers to other recent reviews (5, 6, 8, 9). Also of interest may be new improvements in the Amber family of FFs (10), and, to our knowledge, no new reviews on the OPLS-AA or GROMOS protein FFs have appeared since our previous review in this series.…”

Section: Introductionmentioning

confidence: 99%

Current Status of Protein Force Fields for Molecular Dynamics Simulations

Lopes

Guvench

MacKerell

2014

Methods in Molecular Biology

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168

138

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Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.

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Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies

Cited by 11 publications

References 211 publications

Competition among Li⁺, Na⁺, K⁺, and Rb⁺ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

Competition among Li⁺, Na⁺, K⁺, and Rb⁺ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

Current Status of Protein Force Fields for Molecular Dynamics Simulations

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Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies

Cited by 11 publications

References 211 publications

Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

Current Status of Protein Force Fields for Molecular Dynamics Simulations

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Product

Resources

About

Competition among Li⁺, Na⁺, K⁺, and Rb⁺ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

Competition among Li⁺, Na⁺, K⁺, and Rb⁺ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields