ArticleJournal of chemical theory and computation2017
Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- How well do various QM-derived net atomic charges reproduce the electrostatic potential surrounding a material across multiple geometric conformations?RSC advances · 2025Article
- Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models.Journal of chemical theory and computation · 2023Article
- Time-resolved terahertz-Raman spectroscopy reveals that cations and anions distinctly modify intermolecular interactions of water.Nature chemistry · 2022Article
- Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations.Journal of chemical theory and computation · 2022Article
- Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges.The Journal of chemical physics · 2022Article
- Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity.Accounts of chemical research · 2021Article
- Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.Journal of chemical theory and computation · 2021Article
- Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids.Interface focus · 2019Article
- New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization.RSC advances · 2019Article
- Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019Article
- Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings.Chemical science · 2019Article
- Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.Chemical reviews · 2019Review
- Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.Annual review of biophysics · 2019Review
- Accurate Biomolecular Simulations Account for Electronic Polarization.Frontiers in molecular biosciences · 2019Article
- Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.Chemical science · 2018Article
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8 authors.
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Abstract
We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration ("peek"), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter ω, can be made at almost no cost. This method is denoted by TCG-n(ω). Black-box adaptive methods to find good choices of ω are provided and discussed. Results show that TPCG-3(ω) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(ω) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production algorithm. The T(P)CG-1(ω) level provides less accurate solutions for inhomogeneous systems, but its applicability to well-conditioned problems such as water is remarkable, with only two matrix-vector product evaluations.
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