Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
Published 2018 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
Authors
Keywords
-
Journal
Chemical Science
Volume 9, Issue 4, Pages 956-972
Publisher
Royal Society of Chemistry (RSC)
Online
2017-11-27
DOI
10.1039/c7sc04531j
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Computational and experimental characterization of a pyrrolidinium-based ionic liquid for electrolyte applications
- (2017) Hedieh Torabifard et al. JOURNAL OF CHEMICAL PHYSICS
- Mapping the Drude polarizable force field onto a multipole and induced dipole model
- (2017) Jing Huang et al. JOURNAL OF CHEMICAL PHYSICS
- The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces
- (2017) Félix Aviat et al. JOURNAL OF CHEMICAL PHYSICS
- Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding
- (2017) Daniele Loco et al. Journal of Chemical Theory and Computation
- Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability
- (2017) Robert M. Parrish et al. Journal of Chemical Theory and Computation
- GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
- (2017) Chigusa Kobayashi et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs
- (2017) Matthew Harger et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
- (2017) Peter Eastman et al. PLoS Computational Biology
- Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
- (2016) Félix Aviat et al. Journal of Chemical Theory and Computation
- A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations
- (2016) Daniele Loco et al. Journal of Chemical Theory and Computation
- Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles
- (2016) Christophe Narth et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields
- (2016) Eric G. Kratz et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins
- (2016) Jing Huang et al. NATURE METHODS
- Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
- (2015) Filippo Lipparini et al. Journal of Chemical Theory and Computation
- Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
- (2015) Michael J. Robertson et al. Journal of Chemical Theory and Computation
- Achieving Linear Scaling in Computational Cost for a Fully Polarizable MM/Continuum Embedding
- (2015) Stefano Caprasecca et al. Journal of Chemical Theory and Computation
- Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald
- (2015) Louis Lagardère et al. Journal of Chemical Theory and Computation
- ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
- (2015) James A. Maier et al. Journal of Chemical Theory and Computation
- Quantum, classical, and hybrid QM/MM calculations in solution: General implementation of the ddCOSMO linear scaling strategy
- (2014) Filippo Lipparini et al. JOURNAL OF CHEMICAL PHYSICS
- A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulations
- (2014) Mike Devereux et al. Journal of Chemical Theory and Computation
- Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations
- (2014) Filippo Lipparini et al. Journal of Chemical Theory and Computation
- GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations
- (2014) Robert E. Duke et al. Journal of Chemical Theory and Computation
- Hydration gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics
- (2014) Aude Marjolin et al. JOURNAL OF MOLECULAR MODELING
- Development of AMOEBA Force Field for 1,3-Dimethylimidazolium Based Ionic Liquids
- (2014) Oleg N. Starovoytov et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Quantum Calculations in Solution for Large to Very Large Molecules: A New Linear Scaling QM/Continuum Approach
- (2014) Filippo Lipparini et al. Journal of Physical Chemistry Letters
- Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins
- (2013) Yue Shi et al. Journal of Chemical Theory and Computation
- Fast Domain Decomposition Algorithm for Continuum Solvation Models: Energy and First Derivatives
- (2013) Filippo Lipparini et al. Journal of Chemical Theory and Computation
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
- (2013) Romelia Salomon-Ferrer et al. Journal of Chemical Theory and Computation
- New faster CHARMM molecular dynamics engine
- (2013) Antti-Pekka Hynninen et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Systematic Improvement of a Classical Molecular Model of Water
- (2013) Lee-Ping Wang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations
- (2012) Scott Le Grand et al. COMPUTER PHYSICS COMMUNICATIONS
- New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field
- (2012) Maria M. Reif et al. Journal of Chemical Theory and Computation
- Development of Polarizable Models for Molecular Mechanical Calculations. 3. Polarizable Water Models Conforming to Thole Polarization Screening Schemes
- (2012) Jun Wang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies
- (2012) Aude Marjolin et al. THEORETICAL CHEMISTRY ACCOUNTS
- New functionalities in the GROMOS biomolecular simulation software
- (2011) Anna-Pitschna E. Kunz et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- A new force field model of 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid and acetonitrile mixtures
- (2011) Vitaly V. Chaban et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
- (2010) M. Valiev et al. COMPUTER PHYSICS COMMUNICATIONS
- Current Status of the AMOEBA Polarizable Force Field
- (2010) Jay W. Ponder et al. JOURNAL OF PHYSICAL CHEMISTRY B
- High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD
- (2010) Wei Jiang et al. Journal of Physical Chemistry Letters
- Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation
- (2009) Anders M. N. Niklasson et al. JOURNAL OF CHEMICAL PHYSICS
- Electronic Energy Transfer in Condensed Phase Studied by a Polarizable QM/MM Model
- (2009) Carles Curutchet et al. Journal of Chemical Theory and Computation
- CHARMM: The biomolecular simulation program
- (2009) B. R. Brooks et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Application of a New Cyclic Guanidinium Ionic Liquid on Dye-Sensitized Solar Cells (DSCs)
- (2009) Dongmei Li et al. LANGMUIR
- A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes
- (2008) Jerry M. Parks et al. JOURNAL OF CHEMICAL PHYSICS
- Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
- (2008) L. Zheng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now