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Wydział Fizyki Technicznej i Matematyki Stosowanej
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Wybrane publikacje

  • Advanced Potential Energy Surfaces for Molecular Simulation

    • A. Albaugh
    • H. Boateng
    • R. Bradshaw
    • O. Demerdash
    • J. Dziedzic
    • Y. Mao
    • D. Margul
    • J. Swails
    • Q. Zeng
    • D. Case
    • P. Eastman
    • J. Essex
    • M. Head-Gordon
    • V. Pande
    • J. Ponder
    • Y. Shao
    • C. Skylaris
    • I. Todorov
    • M. Tuckerman
    • T. Head-Gordon

    - JOURNAL OF PHYSICAL CHEMISTRY B - 2016

    Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...

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  • TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field

    • J. Dziedzic
    • Y. Mao
    • Y. Shao
    • J. Ponder
    • T. Head-Gordon
    • M. Head-Gordon
    • C. Skylaris

    - JOURNAL OF CHEMICAL PHYSICS - 2016

    We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...

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  • Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis

    • Y. Mao
    • Y. Shao
    • J. Dziedzic
    • C. Skylaris
    • T. Head-Gordon
    • M. Head-Gordon

    - Journal of Chemical Theory and Computation - 2017

    The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...

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