ArticleChemical science2018
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.
Article in Chemical science, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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80 citing papers in PubMed.
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- Dual-LAO for calculating fast and robust relative binding free energies of simple and complex transformations.Communications chemistry · 2026Article
- Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments.bioRxiv : the preprint server for biology · 2026Article
- Solvation-induced local structure in liquids probed by high-harmonic spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- The Q-AMOEBA (CF) Polarizable Potential.The journal of physical chemistry letters · 2025Article
- High-Resolution Molecular-Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2).Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Histidine 73 methylation coordinates β-actin plasticity in response to key environmental factors.Nature communications · 2025Article
- Modelling Lithium-Ion Transport Properties in Sulfoxides and Sulfones with Polarizable Molecular Dynamics and NMR Spectroscopy.ChemPlusChem · 2025Article
- Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations.Journal of chemical theory and computation · 2025Article
- Article
- Simulations of γ-Valerolactone Solvents and Electrolytes for Lithium Batteries Using Polarizable Molecular Dynamics.Molecules (Basel, Switzerland) · 2025Article
- Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins.Communications biology · 2024Article
- A Polarizable Forcefields for Glyoxal Acetals as Electrolyte Components for Lithium-Ion Batteries.ChemistryOpen · 2024Article
- Sequence-Selective Recognition of the d(GGCGCC)ACS omega · 2024Article
- Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes.Journal of chemical theory and computation · 2024Article
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.The Journal of chemical physics · 2024Article
- Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP.The Journal of chemical physics · 2024Article
- Incorporating Neural Networks into the AMOEBA Polarizable Force Field.The journal of physical chemistry. B · 2024Article
20 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
Abstract
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated
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