ArticleJournal of chemical theory and computation2012
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating.Journal of chemical information and modeling · 2025Article
- Quantitative insights into the mechanism of proton conduction and selectivity for the human voltage-gated proton channel Hv1.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package.The journal of physical chemistry. B · 2024Article
- Transient water wires mediate selective proton transport in designed channel proteins.Nature chemistry · 2023Article
- Acidic Conditions Impact Hydrophobe Transfer across the Oil-Water Interface in Unusual Ways.The journal of physical chemistry. B · 2023Article
- Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins.The journal of physical chemistry. B · 2022Article
- Accurate pThe journal of physical chemistry. B · 2022Article
- Proton coupling and the multiscale kinetic mechanism of a peptide transporter.Biophysical journal · 2022Article
- Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.Journal of the American Chemical Society · 2022Article
- A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The future of biomolecular simulation in the pharmaceutical industry: what we can learn from aerodynamics modelling and weather prediction. Part 1. understanding the physical and computational complexity of in silico drug design.Acta crystallographica. Section D, Structural biology · 2021Article
- Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory.The journal of physical chemistry. B · 2021Article
- Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics.Journal of the American Chemical Society · 2020Article
- A Computational Swiss Army Knife Approach to Unraveling the Secrets of Proton Movement through SERCA.Biophysical journal · 2020Article
- Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale.Biophysical journal · 2020Article
- Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra.The journal of physical chemistry. B · 2020Article
- Local conformational dynamics regulating transport properties of a ClJournal of computational chemistry · 2020Article
- Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules.Journal of the American Chemical Society · 2019Article
- Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel.Journal of the American Chemical Society · 2019Article
- Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux.Journal of the American Chemical Society · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.
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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.