Code publications

If you use Tinker-HP, please cite the main publication:

  • Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Polarizable Force Fields. L. Lagardère, L.-H. Jolly, F. Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders, N. Gresh, Y. Maday, P. Ren, J. W. Ponder, J.-P. Piquemal, Chem. Sci., 2018, 9, 956-972 (Open Access), DOI: 10.1039/C7SC04531J

If you use the GPU version, please also cite:

  • Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. O. Adjoua,  L. Lagardère, L.-H. Jolly, Arnaud Durocher, Z. Wang, T. Very, I. Dupays, T. Jaffrelot Inizan, F. Célerse, P. Ren, J. Ponder, J-P. Piquemal, J. Chem. Theory. Comput., 2021, 17, 4, 2034–2053 (Open Access) (COVER), DOI: 10.1021/acs.jctc.0c01164

If you use the vectorized CPU (AVX512) version, please also cite:

  • Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0].
    L. H. Jolly, A. Duran, L. Lagardère, J. W. Ponder, P. Y. Ren, J.-P. Piquemal, Living Journal of Computational Molecular Science, 2019, 1 (2), 10409  (Open Access) DOI: 10.33011/livecoms.1.2.10409

Technology (selected publications)

  • Scalable evaluation of the polarization energy and associated forces in polarizable molecular dynamics: I. towards massively parallel direct space computations.
    F. Lipparini, L. Lagardère, B. Stamm, E. Cancès, M. Schnieders, P. Y. Ren, Y. Maday, J.-P. Piquemal, J. Chem. Theory. Comput., 2014, 10, 1638-1651[PDF][PMC Free Text], DOI: 10.1021/ct401096t
  • Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.L. Lagardère, F. Lipparini, E. Polack, B. Stamm, E. Cancès, M. Schnieders, P. Y. Ren, Y. Maday, J.-P. Piquemal, J.Chem. Theory. Comput., 2015, 11, 2589-2599 [PMC Free Text], DOI: 10.1021/acs.jctc.5b00171
  • Polarizable Molecular Dynamics in a Polarizable Continuum Solvent.
    F. Lipparini, L. Lagardère, C. Raynaud, B. Stamm, E. Cancès, M. Schnieders, P. Y. Ren, B. Mennucci, Y. Maday, J.-P. Piquemal, J. Chem. Theory. Comput., 2015, 11, 623-634 [PMC Free Text], DOI: 10.1021/ct500998q
  • Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding.
    D. Loco, L. Lagardère, S. Caprasecca, F. Lipparini, B. Mennucci, J.-P. Piquemal, J. Chem. Theory. Comput, 2017, 13, 4025-4033 (Open Access), DOI: 10.1021/acs.jctc.7b00572
  • A QM/MM approach using the AMOEBA polarizable embedding: from ground state energies to electronic excitations.
    D. Loco, E. Polack, S. Caprasecca, L. Lagardère, F. Lipparini, J.-P. Piquemal, B. Mennucci, J. Chem. Theory. Comput., 2016, 12, 3654-3661 [HAL] DOI: 10.1021/acs.jctc.6b00385
  • Truncated Conjugate Gradient (TCG): an optimal strategy for the analytical evaluation of the many-body polarization energy and forces in molecular simulations. F. Aviat, A. Levitt, Y. Maday, B. Stamm, P. Y. Ren, J. W. Ponder, L. Lagardère, J.-P.Piquemal, J. Chem. Theory. Comput., 2017, 13, 180-190 (Open Access), DOI: 10.1021/acs.jctc.6b00981
  • Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs.
    M. Harger, D. Li, Z. Wang, K. Dalby, L. Lagardère, J.-P. Piquemal, J. Ponder, P. Ren, J. Comput. Chem., 2017, 38, 2047-2055[PDF] [PMC Free Text], DOI: 10.1002/jcc.24853
  • Tinker 8: Software Tools for Molecular Design.
    J. A. Rackers, Z. Wang, C. Lu, M. L. Maury, L. Lagardère, M. J. Schnieders, J.-P. Piquemal, P. Ren, J. W. Ponder,  J. Chem. Theory. Comput., 2018, 14 (10), 5273–5289 [PMC Free Text][PDF], DOI: 10.1021/acs.jctc.8b00529
  • Massively parallel implementation of Steered Molecular Dynamics in Tinker-HP: polarizable versus non-polarizable simulations.
    F. Célerse, L. Lagardère, E. Derat, J.-P.Piquemal, J. Chem. Theory. Comput., 2019, 15, 3694-3709 [ChemRxiv], DOI: 10.1021/acs.jctc.9b00199
  • Pushing the limits of Multiple-Timestep Strategies for Polarizable Point Dipole Molecular Dynamics.
    L. Lagardère, F. Aviat, J.-P. Piquemal, J. Phys. Chem. Lett., 2019, 10, 2593−2599 [PDF], DOI: 10.1021/acs.jpclett.9b00901
  • Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings.
    D. Loco, L. Lagardère, G. A. Cisneros, G. Scalmani, M. Frisch, F. Lipparini, B. Mennucci, J.-P. Piquemal, Chem. Sci., 2019, 10, 7200-7211 (Open Access), DOI: 10.1039/C9SC01745C
  • Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model.P. P. Poier, L. Lagardère, J.-P. Piquemal, F. Jensen, J. Chem. Theory. Comput., 2019, 15, 11, 6213-6224 [ChemrXiv], DOI: 10.1021/acs.jctc.9b00721
  • AMOEBA+ Classical Potential for Modeling Molecular Interactions.
    C. Liu, J.-P. Piquemal, P. Ren, J. Chem. Theory. Comput., 2019, 15, 4122-4139 [ChemRxiv][PMC Free Text], DOI: 10.1021/acs.jctc.9b00261
  • Velocity jump processes : an alternative to multi-time-step methods for faster and accurate molecular dynamics simulations.
    P. Monmarché, J. Weisman, L. Lagardère, J.-P. Piquemal, J. Chem. Phys., 2020,  153, 024101 [ArXiv], DOI: 10.1063/5.0005060
  • Implementation of Geometry Dependent Charge Flux into the Polarizable AMOEBA+ Potential.
    C. Liu, J.-P. Piquemal, P. Ren, J. Phys. Chem. Lett., 2020, 11, 419-426 [ChemRxiv][PMC Free Text], DOI: 10.1021/acs.jpclett.9b03489
  • High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling.T. Jaffrelot Inizan, F. Célerse, O. Adjoua, D. El Ahdab, L.-H. Jolly, C. Liu, P. Ren, M. Montes, N. Lagarde, L. Lagardère, P. Monmarché, J.-P. Piquemal, Chem. Sci., 2021, 12, 4889 – 4907 (Open Access), DOI: 10.1039/D1SC00145K
  • Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. R. A. Corrigan, G. Qi, T. Casavant, A. Thiel, J. Lynn, B. Walker, L. Lagardère, J.-P. Piquemal, J. W. Ponder, P. Ren, M. J. Schnieders, J. Chem. Theory Comput., 2021, 17, 4, 2323–2341, DOI: 10.1021/acs.jctc.0c01286
  • Nuclear Quantum Effects in liquid water at near classical computational cost using the adaptive Quantum Thermal Bath.
    N. Mauger, T. Plé, L. Lagardère, S. Bonella, E. Mangaud, J.-P. Piquemal, S. Huppert, J. Phys. Chem. Lett., 2021, 12, 34, 8285–8291 [ArXiv], DOI: 10.1021/acs.jpclett.1c01722
  • Atomistic Polarizable embeddings: energy, dynamics, spectroscopy and reactivity.
    D. Loco, L. Lagardère, O.  Adjoua, J.-P. Piquemal, Acc. Chem. Res., 2021, 54, 13, 2812–2822 (Open Access) (COVER), DOI: 10.1021/acs.accounts.0c00662
  • An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems.
    F. Célerse, T. Jaffrelot Inizan,  L. Lagardère, O. Adjoua, P. Monmarché, Y. Miao, E. Derat, J.-P. Piquemal, J. Chem. Theory Comput., 2022, 18, 2, 968–977 (COVER)[ChemRxiv], DOI: 10.1021/acs.jctc.1c01024
  • O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems.
    P. P. Poier, L. Lagardère, J.-P. Piquemal, J. Chem. Theory Comput., 2022, 18, 3, 1633–1645 (COVER)[ChemRxiv], DOI: 10.1021/acs.jctc.1c01291
  • Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory.
    P. P. Poier, T. Jaffrelot Inizan, O. Adjoua, L. Lagardère, J.-P. Piquemal, J. Phys. Chem. Lett.,  2022, 13, 19, 4381–4388 [ArXiv], DOI: 10.1021/acs.jpclett.2c00936
  • Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: I. Enabling Condensed Phase Molecular Dynamics Simulations. S. Naseem Kahn, L. Lagardère, C. Narth, G. A. Cisneros, P. Ren, N. Gresh, J.-P. Piquemal, 2022, 18, 6, 3607–3621, [ArXiv], DOI: 10.1021/acs.jctc.2c00029
  • Improving Condensed Phase Water Dynamics with Explicit Nuclear Quantum Effects: the Polarizable Q-AMOEBA Force Field.
    N. Mauger, T. Plé, L. Lagardère, S. Huppert, J.-P. Piquemal, J. Phys. Chem. B, 2022, online (Biomolecular Electrostatic Phenomena Virtual Special Issue) [ArXiv], DOI: 10.1021/acs.jpcb.2c04454
  • Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including long-range effects. T. Jaffrelot Inizan, T. Plé, O. Adjoua, P. Ren, H. Gökcan, O. Isayev, L. Lagardère, Jean-Philip Piquemal, 2022, DOI: https://arxiv.org/abs/2207.14276