ReviewThe journal of physical chemistry. B2016
Advanced Potential Energy Surfaces for Molecular Simulation.
Review in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
24 citing papers in PubMed.
- Mechanism of thermal oxidation into volatile compounds from (E)-4-decenal: A density functional theory study.Food chemistry: X · 2024Article
- Identification of Peptidoglycan Glycosyltransferase FtsI as a Potential Drug Target againstCurrent pharmaceutical design · 2024Article
- The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors.Mini reviews in medicinal chemistry · 2024Review
- Data scheme and data format for transferable force fields for molecular simulation.Scientific data · 2023Article
- Non-covalent interactions from a Quantum Chemical Topology perspective.Journal of molecular modeling · 2022Article
- Two Liberibacter Proteins Combine to Suppress Critical Innate Immune Defenses in Citrus.Frontiers in plant science · 2022Article
- Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study.JACS Au · 2021Article
- Extension of an Atom-Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts.The journal of physical chemistry. A · 2021Article
- On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces.Interface focus · 2020Article
- A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics.Journal of computational chemistry · 2020Article
- Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids.Interface focus · 2019Article
- Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model.Journal of chemical theory and computation · 2019Article
- Study of the Wilcox torsion balance in solution for a Tröger's base derivative with hexyl-and heptyl substituents using a combined molecular mechanics and quantum chemistry approach.Journal of molecular modeling · 2019Article
- Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.Journal of computer-aided molecular design · 2019Review
- Toward Learned Chemical Perception of Force Field Typing Rules.Journal of chemical theory and computation · 2019Article
- A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.Molecules (Basel, Switzerland) · 2018Article
- The strengths and limitations of effective centroid force models explored by studying isotopic effects in liquid water.The Journal of chemical physics · 2018Article
- Chloride Ion Transport by theFrontiers in chemistry · 2018Article
- Mapping the Drude polarizable force field onto a multipole and induced dipole model.The Journal of chemical physics · 2017Article
- OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.PLoS computational biology · 2017Article
Corrections and comments
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Authors and funding
21 authors.
Funding
Abstract
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.