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Timothy J. Giese
Researcher at Rutgers University
Publications - 53
Citations - 1620
Timothy J. Giese is an academic researcher from Rutgers University. The author has contributed to research in topics: Medicine & Ab initio. The author has an hindex of 24, co-authored 44 publications receiving 1180 citations. Previous affiliations of Timothy J. Giese include University of Minnesota.
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Journal ArticleDOI
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
Tai-Sung Lee,David S. Cerutti,Daniel J. Mermelstein,Charles Y. Lin,Scott LeGrand,Timothy J. Giese,Adrian E. Roitberg,David A. Case,Ross C. Walker,Darrin M. York +9 more
TL;DR: Progress is reported in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber, including free energy perturbation and thermodynamic integration methods with support for nonlinear soft-core potential and parameter interpolation transformation pathways.
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Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.
Tai-Sung Lee,Bryce K. Allen,Timothy J. Giese,Zhenyu Guo,Pengfei Li,Charles Y. Lin,T. Dwight McGee,David A. Pearlman,Brian K. Radak,Yujun Tao,Hsu Chun Tsai,Huafeng Xu,Woody Sherman,Darrin M. York +13 more
TL;DR: A contemporary overview of the scientific, technical, and practical issues associated with running relative BFE simulations in AMBER20 is provided, with a focus on real-world drug discovery applications.
Journal ArticleDOI
Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations.
Timothy J. Giese,Darrin M. York +1 more
TL;DR: A new model for nonelectrostatic nonbonded interactions in QMMM calculations that overcomes many of these problems is proposed, based on a scaled overlap model for repulsive exchange and attractive dispersion interactions that is a function of atomic charge.
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A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields.
Timothy J. Giese,Haoyuan Chen,Thakshila Dissanayake,George M. Giambaşu,Hugh Heldenbrand,Ming Huang,Erich R. Kuechler,Tai-Sung Lee,Maria T. Panteva,Brian K. Radak,Darrin M. York +10 more
TL;DR: A new hybrid molecular orbital/density-functional modified divide-and-conquer (mDC) approach that allows the linear-scaling calculation of very large quantum systems and provides a powerful framework from which linear- scaling force fields for molecular simulations can be developed.
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Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits
Timothy J. Giese,Darrin M. York +1 more
TL;DR: It is demonstrated that many-body force field models based solely on pairwise Coulomb screening cannot simultaneously reproduce both gas-phase and condensed-phase polarizability limits, and that coupling with non-classical many- body effects, in particular exchange terms, may be important.