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.

scholarly journals Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field

2021 ◽  
Author(s):  
Sebastian Falkner ◽  
Nadine Schwierz
Keyword(s):  
Force Field ◽  
Water Exchange ◽  
Force Fields ◽  
Hydration Shell ◽  
Water Model ◽  
Polarizable Force Fields ◽  
Ionic Force ◽  
Influence Of Water ◽  
Biomolecular Simulations ◽  
Dynamics Simulations

Water exchange between the first and second hydration shell is essential for the role of Mg2+ in biochemical processes. In order to provide microscopic insights into the exchange mechanism, we resolve the exchange pathways by all-atom molecular dynamics simulations and transition path sampling. Since the exchange kinetics relies on the choice of the water model and the ionic force field, we systematically investigate the influence of seven different polarizable and non-polarizable water and three different Mg2+ models. In all cases, water exchange can occur either via an indirect or direct mechanism (exchanging molecules occupy different/same position on water octahedron). In addition, the results reveal a crossover from an interchange dissociative (Id) to an associative (Ia) reaction mechanism dependent on the range of the Mg2+-water interaction potential of the respective force field. Standard non-polarizable force fields follow the Id mechanism in agreement with experimental results. By contrast, polarizable and long-ranged non-polarizable force fields follow the Ia mechanism. Our results provide a comprehensive view on the influence of the water model and ionic force field on the exchange dynamics and the foundation to assess the choice of the force field in biomolecular simulations.

scholarly journals Further refinements of next-generation force fields — Nonempirical localization of off-centered points in molecules

2013 ◽  
Vol 91 (9) ◽  
pp. 804-810 ◽  
Author(s):  
Robin Chaudret ◽  
Nohad Gresh ◽  
G. Andrés Cisneros ◽  
Anthony Scemama ◽  
Jean-Philip Piquemal
Keyword(s):  
Force Fields ◽  
Lone Pair ◽  
Basis Sets ◽  
Water Model ◽  
Electrostatic Model ◽  
Next Generation ◽  
Biologically Relevant ◽  
Localization Function ◽  
Polarizable Force Fields ◽  
Lone Pairs

In the present work, we investigate different possibilities for the nonempirical localization of nonatomic centers within the context of the design of new generation polarizable force fields. To do so, the positions of electron localization function (ELF) and electron pair localization function (EPLF) attractors and of Boys orbital centroids are determined for a set of thirteen saturated and conjugated biologically relevant molecules. We consider the similarities and differences in the representations of localized lone pairs and π delocalized systems by these approaches, as well as the effects of the basis sets and of the level of quantum chemistry (QC). All three methods give consistent results upon dealing with the localized lone pairs. Concerning aromatic systems, whereas ELF and EPLF methods give mutually consistent results, the Boys scheme breaks the symmetry by alternating the electron distributions along the C–C bonds providing a different distribution of off-centered points. We then investigate the influence of lone pair localization in the water model of the Gaussian electrostatic model/sum of interactions between fragments ab initio computed (GEM/SIBFA) polarizable force field, which embodies an explicit representation of the lone pairs. This is done, in a series of mono- and poly-hydrated Zn(II) complexes, by comparing the overlap-dependent repulsion (Erep) and charge-transfer (Ect) contributions to their QC counterparts. We resort to either the current GEM/SIBFA water lone pair internal coordinates or to the ones derived from the previously mentioned localization procedures. The latter enables closer reproductions by Erep and Ect (GEM/SIBFA) of their exchange repulsion (Eexch) and Ect QC counterparts. The present preliminary results show that QC localization procedures can be used to derive accurate, nonempirical positions for off-centered points intervening in the formulation of the overlap-dependent contributions of next-generation polarizable force fields.

scholarly journals New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

2018 ◽  
Vol 20 (13) ◽  
pp. 8432-8449 ◽  
Author(s):  
Jejoong Yoo ◽  
Aleksei Aksimentiev
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Biomolecular Systems ◽  
Recent Advances ◽  
Dynamics Simulations

Recent advances in parallel computing have pushed all-atom molecular dynamics simulations into an untested territory. This article reviews the applications of the NBFIX approach for testing and improving molecular dynamics force fields and discuses the implications of the NBFIX corrections for simulations of various biomolecular systems.

Immunotherapy for regional, recurrent and metastatic head and neck cancer: recent advances and future directions

2020 ◽  
pp. 60-69
Author(s):  
Z. A.-G. Radzhabova ◽  
M. Д. Kotov ◽  
A. S. Mitrofanov ◽  
Z. S. Bekyasheva ◽  
E. V. Levchenko
Keyword(s):  
Head And Neck Cancer ◽  
Head And Neck ◽  
Neck Cancer ◽  
Future Directions ◽  
Recent Advances

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>

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