Polarizable force fields for biomolecular simulations: Recent advances and applications
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics,
including electronic polarization. Due to recent advances in physical models, simulation …
including electronic polarization. Due to recent advances in physical models, simulation …
New developments in force fields for biomolecular simulations
PS Nerenberg, T Head-Gordon - Current opinion in structural biology, 2018 - Elsevier
Highlights•Biomolecular force fields (FFs) have progressed rapidly in the past five
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …
Development of an advanced force field for water using variational energy decomposition analysis
Given the piecewise approach to modeling intermolecular interactions for force fields, they
can be difficult to parametrize since they are fit to data like total energies that only indirectly …
can be difficult to parametrize since they are fit to data like total energies that only indirectly …
Accurate biomolecular simulations account for electronic polarization
J Melcr, JP Piquemal - Frontiers in molecular biosciences, 2019 - frontiersin.org
In this perspective, we discuss where and how accounting for electronic many-body
polarization affects the accuracy of classical molecular dynamics simulations of …
polarization affects the accuracy of classical molecular dynamics simulations of …
Force fields for small molecules
FY Lin, AD MacKerell - Biomolecular simulations: Methods and protocols, 2019 - Springer
Molecular dynamics (MD) simulations have been widely applied to computer-aided drug
design (CADD). While MD has been used in a variety of applications such as free energy …
design (CADD). While MD has been used in a variety of applications such as free energy …
Advanced models for water simulations
O Demerdash, LP Wang… - Wiley Interdisciplinary …, 2018 - Wiley Online Library
Molecular simulations of water using classical, molecular mechanic potential energy
functions have enjoyed a 50‐year history of development, and much has been learned …
functions have enjoyed a 50‐year history of development, and much has been learned …
Force Decomposition Analysis: A method to decompose intermolecular forces into physically relevant component contributions
Computational quantum chemistry can be more than just numerical experiments when
methods are specifically adapted to investigate chemical concepts. One important example …
methods are specifically adapted to investigate chemical concepts. One important example …
Improvements to the AMOEBA force field by introducing anisotropic atomic polarizability of the water molecule
AK Das, ON Demerdash… - Journal of chemical …, 2018 - ACS Publications
In this work, we have developed an anisotropic polarizable model for the AMOEBA force
field that is derived from electrostatic fitting on a gas phase water molecule as the primary …
field that is derived from electrostatic fitting on a gas phase water molecule as the primary …
Symmetrized drude oscillator force fields improve numerical performance of polarizable molecular dynamics
A Dodin, PL Geissler - Journal of Chemical Theory and …, 2023 - ACS Publications
Drude oscillator potentials are a popular and computationally efficient class of polarizable
models that represent each polarizable atom as a positively charged Drude core …
models that represent each polarizable atom as a positively charged Drude core …
Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
MM Ghahremanpour, PJ van Maaren… - Journal of chemical …, 2018 - ACS Publications
Gas-phase electric properties of molecules can be computed routinely using wave function
methods or density functional theory (DFT). However, these methods remain …
methods or density functional theory (DFT). However, these methods remain …