Automation of AMOEBA polarizable force field for small molecules: Poltype 2
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26954
Abstract: A next‐generation protocol (Poltype 2) has been developed which automatically generates AMOEBA polarizable force field parameters for small molecules. Both features and computational efficiency have been drastically improved. Notable advances include improved database transferability using… read more here.
Keywords: polarizable force; free energy; torsion; small molecules ... See more keywords
Dynamics of ions in a water drop using the AMOEBA polarizable force field
Sign Up to like & getrecommendations! Published in 2017 at "Chemical Physics Letters"
DOI: 10.1016/j.cplett.2017.01.024
Abstract: Abstract Various ions carrying a charge from −2 to +3 were confined in a drop of 100 water molecules as a way to model coordination properties inside the cluster and at the interface. The behavior… read more here.
Keywords: force field; drop; water; amoeba polarizable ... See more keywords
Polarizable Force Field of Intrinsically Disordered Proteins with CMAP and Reweighting Optimization
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00835
Abstract: Intrinsically disordered proteins (IDPs) are highly structurally heterogeneous without a specific tertiary structure under physiology conditions and play key roles in the development of human diseases. Due to the characteristics of diverse conformations, as one… read more here.
Keywords: polarizable force; intrinsically disordered; disordered proteins; force ... See more keywords
Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.3c00250
Abstract: Polarizable force fields, in particular, the Drude polarizable force field (Drude FF), may hold the key to more accurately modeling biomolecules with molecular dynamics simulations by explicitly accounting for atomic polarizability. Previous work has shown… read more here.
Keywords: polarizable force; gacc tetranucleotide; force; drude polarizable ... See more keywords
An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c01024
Abstract: We introduce a novel multilevel enhanced sampling strategy grounded on Gaussian-accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We introduce the new "dual-water" mode and its… read more here.
Keywords: enhanced sampling; multilevel enhanced; polarizable force; force ... See more keywords
Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.7b00067
Abstract: Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are… read more here.
Keywords: force field; dna; field; force ... See more keywords
Drude Polarizable Force Field Parametrization of Carboxylate and N-acetyl Amine Carbohydrate Derivatives.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00327
Abstract: In this work, we report the development of Drude polarizable force-field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of existing Drude polarizable carbohydrate force field. The force field parameters have been… read more here.
Keywords: force field; drude polarizable; field parameters; force ... See more keywords
Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00721
Abstract: 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… read more here.
Keywords: molecular dynamics; energy; bond capacity; force ... See more keywords