scholarly journals Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

2014 ◽  
Vol 5 (18) ◽  
pp. 3144-3150 ◽  
Author(s):  
Jing Huang ◽  
Pedro E. M. Lopes ◽  
Benoît Roux ◽  
Alexander D. MacKerell
Keyword(s):  
Force Fields ◽  
Oscillator Model ◽  
Polarizable Force Fields ◽  
Recent Advances

scholarly journals Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

2019 ◽  
Vol 48 (1) ◽  
pp. 371-394 ◽  
Author(s):  
Zhifeng Jing ◽  
Chengwen Liu ◽  
Sara Y. Cheng ◽  
Rui Qi ◽  
Brandon D. Walker ◽  
...  
Keyword(s):  
Force Fields ◽  
Intermolecular Forces ◽  
Physical Models ◽  
Biomolecular Systems ◽  
Future Directions ◽  
Biologically Relevant ◽  
Polarizable Force Fields ◽  
Recent Advances ◽  
Accurate Treatment ◽  
Biomolecular Simulations

Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.

Molecular Dynamics Using Non-Variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model

2019 ◽  
Author(s):  
Pier Paolo Poier ◽  
Louis Lagardere ◽  
Jean-Philip Piquemal ◽  
Frank Jensen
Keyword(s):  
Boundary Conditions ◽  
Periodic Boundary ◽  
Force Fields ◽  
Periodic Boundary Conditions ◽  
Computational Effort ◽  
Polarizable Force Fields ◽  
Energy Models ◽  
Capacity Model ◽  
Energy Gradient ◽  
Polarization Models

<div> <div> <div> <p>We extend the framework for polarizable force fields to include the case where the electrostatic multipoles are not determined by a variational minimization of the electrostatic energy. Such models formally require that the polarization response is calculated for all possible geometrical perturbations in order to obtain the energy gradient required for performing molecular dynamics simulations. </p><div> <div> <div> <p>By making use of a Lagrange formalism, however, this computational demanding task can be re- placed by solving a single equation similar to that for determining the electrostatic variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p><div><div><div> </div> </div> </div> <p> </p><div> <div> <div> <p>variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p> </div> </div> </div> </div> </div> </div> </div> </div> </div>

scholarly journals High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Polarizable Force Fields ◽  
Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

scholarly journals The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

2020 ◽  
Author(s):  
Richard T Bradshaw ◽  
Jacek Dziedzic ◽  
Chris-Kriton Skylaris ◽  
Jonathan W. Essex
Keyword(s):  
Electric Fields ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Force Fields ◽  
Prolyl Isomerase ◽  
Peptidyl Prolyl Isomerase ◽  
Polarizable Force Field ◽  
Polarizable Force Fields ◽  
Protein Active Sites ◽  
Dynamics Simulations

<div><div><div><p>Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric fields present inside the active site of the peptidyl-prolyl isomerase cyclophilin A. We compare the molecular mechanical electric fields to those calculated with a fully first principles quantum mechanical (QM) representation of the protein, solvent, and ions, and find that AMOEBA consistently shows far greater correlation with the QM electric fields than either of the additive force fields tested. Catalytically-relevant fields calculated with AMOEBA were typically smaller than those observed with additive potentials, but were generally consistent with an electrostatically-driven mechanism for catalysis. Our results highlight the accuracy and the potential advantages of using polarizable force fields in systems where accurate electrostatics may be crucial for providing mechanistic insights.</p></div></div></div>

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