This article is about a computer program for molecular dynamics. For other uses, see Tinker (disambiguation).
Tinker, previously stylized as TINKER, is a suite of computer software applications for molecular dynamics simulation. The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics, with some special features for biomolecules. The core of the software is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means.
Tinker works on Windows, macOS, Linux and Unix. The source code is available free of charge to non-commercial users under a proprietary license. The code is written in portable FORTRAN 77, Fortran 95 or CUDA with common extensions, and some C.
Core developers are: (a) the Jay Ponder lab, at the Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri. Laboratory head Ponder is Full Professor of Chemistry, and of Biochemistry & Molecular Biophysics; (b) the Pengyu Ren lab , at the Department of Biomedical Engineering University of Texas in Austin, Austin, Texas. Laboratory head Ren is Full Professor of Biomedical Engineering; (c) Jean-Philip Piquemal's research team at Laboratoire de Chimie Théorique, Department of Chemistry, Sorbonne University, Paris, France. Research team head Piquemal is Full Professor of Theoretical Chemistry.
The Tinker package is based on several related codes: (a) the canonical Tinker, version 8, (b) the Tinker9 package as a direct extension of canonical Tinker to GPU systems, (c) the Tinker-HP package for massively parallel MPI applications on hybrid CPU and GPU-based systems, (d) Tinker-FFE for visualization of Tinker calculations via a Java-based graphical interface, and (e) the Tinker-OpenMM package for Tinker's use with GPUs via an interface for the OpenMM software. All of the Tinker codes are available from the TinkerTools organization site on GitHub. Additional information is available from the TinkerTools community web site.
Programs are provided to perform many functions including:
Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F.; Harger, Matthew; Torabifard, Hedieh; Cisneros, Andrés; Schnieders, Michael; Gresh, Nohad; Maday, Yvon; Ren, Pengyu; Ponder, Jay; Piquemal, Jean-Philip (2018). "Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems". Chemical Science. 9 (4): 956–972. doi:10.1039/C7SC04531J. PMC5909332. PMID 29732110.
Adjoua, Olivier; Lagardère, Louis; Jolly, Luc-Henri; Durocher, Arnaud; Wang, Zhi; Very, Thibaut F.; Dupays, Isabelle; Jaffrelot Inizan, Theo; Célerse, Frédéric; Ren, Pengyu; Ponder, Jay; Piquemal, Jean-Philip (2021). "Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields". Journal of Chemical Theory and Computation. 17 (4): 2034–2053. doi:10.1021/acs.jctc.0c01164. PMC7654869. PMID 33173801.
Rackers, Joshua A.; Wang, Zhi; Lu, Chao; Maury, Marie L.; Lagardère, Louis; Schnieders, Michael; Piquemal, Jean-Philip; Ren, Pengyu; Ponder, Jay (2018). "Tinker 8: Software Tools for Molecular Design". Journal of Chemical Theory and Computation. 14 (10): 5273–5289. doi:10.1021/acs.jctc.8b00529. PMC6335969. PMID 30176213.
Harger, Matthew; Li, Daniel; Wang, Zhi; Dalby, Kevin; Lagardère, Louis; Piquemal, Jean-Philip; Ponder, Jay W.; Ren, Pengyu (2017). "Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs". Journal of Computational Chemistry. 38 (23): 2047–2055. doi:10.1002/jcc.24853. PMC5539969. PMID 28600826.
Ren, Pengyu; Ponder, Jay W. (2003). "Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation". The Journal of Physical Chemistry B. 107 (24): 5933–5947. doi:10.1021/jp027815+.
Pappu, Rohit V.; Hart, Reece K.; Ponder, Jay W. (1998). "Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization". The Journal of Physical Chemistry B. 102 (48): 9725. CiteSeerX10.1.1.18.1162. doi:10.1021/jp982255t.
Kong, Yong; Ponder, Jay W. (1997). "Calculation of the reaction field due to off-center point multipoles". The Journal of Chemical Physics. 107 (2): 481. Bibcode:1997JChPh.107..481K. doi:10.1063/1.474409.
Dudek, Michael J.; Ponder, Jay W. (1995). "Accurate modeling of the intramolecular electrostatic energy of proteins". Journal of Computational Chemistry. 16 (7): 791. CiteSeerX10.1.1.502.6823. doi:10.1002/jcc.540160702. S2CID 15899639.
Kundrot, Craig E.; Ponder, Jay W.; Richards, Frederic M. (1991). "Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization". Journal of Computational Chemistry. 12 (3): 402. CiteSeerX10.1.1.511.419. doi:10.1002/jcc.540120314. S2CID 53518520.
Ponder, Jay W.; Richards, Frederic M. (1987). "An efficient newton-like method for molecular mechanics energy minimization of large molecules". Journal of Computational Chemistry. 8 (7): 1016. doi:10.1002/jcc.540080710. S2CID 11607431.
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This article is about a computer program for molecular dynamics For other uses see Tinker disambiguation Tinker previously stylized as TINKER is a suite of computer software applications for molecular dynamics simulation The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics with some special features for biomolecules The core of the software is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means TinkerOriginal author s Jay Ponder Pengyu Ren Jean Philip PiquemalDeveloper s Jay Ponder Lab Department of Chemistry Washington University in St Louis Pengyu Ren Lab Department of Biomedical Engineering the University of Texas at Austin Jean Philip Piquemal Sorbonne University Initial releaseNovember 26 1996 27 years ago 1996 11 26 Stable release8 10 2 April 1 2022 2 years ago 2022 04 01 Written inFortran 95 CUDA OpenMP and MPI ParallelOperating systemWindows macOS Linux UnixAvailable inEnglishTypeMolecular dynamicsLicenseProprietary freeware 1 Websitetinkertools wbr orgTinker works on Windows macOS Linux and Unix The source code is available free of charge to non commercial users under a proprietary license The code is written in portable FORTRAN 77 Fortran 95 or CUDA with common extensions and some C Core developers are a the Jay Ponder lab at the Department of Chemistry Washington University in St Louis St Louis Missouri Laboratory head Ponder is Full Professor of Chemistry and of Biochemistry amp Molecular Biophysics b the Pengyu Ren lab at the Department of Biomedical Engineering University of Texas in Austin Austin Texas Laboratory head Ren is Full Professor of Biomedical Engineering c Jean Philip Piquemal s research team at Laboratoire de Chimie Theorique Department of Chemistry Sorbonne University Paris France Research team head Piquemal is Full Professor of Theoretical Chemistry Contents 1 Features 2 Awards 3 See also 4 References 5 License 6 External linksFeatures editThe Tinker package is based on several related codes a the canonical Tinker version 8 b the Tinker9 package as a direct extension of canonical Tinker to GPU systems c the Tinker HP package for massively parallel MPI applications on hybrid CPU and GPU based systems d Tinker FFE for visualization of Tinker calculations via a Java based graphical interface and e the Tinker OpenMM package for Tinker s use with GPUs via an interface for the OpenMM software All of the Tinker codes are available from the TinkerTools organization site on GitHub Additional information is available from the TinkerTools community web site Programs are provided to perform many functions including energy minimizing over Cartesian coordinates torsional angles or rigid bodies via conjugate gradient variable metric or a truncated Newton method molecular stochastic and rigid body dynamics with periodic boundaries and control of temperature and pressure normal mode vibrational analysis distance geometry including an efficient random pairwise metrization building protein and nucleic acid structures from sequence simulated annealing with various cooling protocols analysis and breakdown of single point potential energies verification of analytical derivatives of standard and user defined potentials location of a transition state between two minima full energy surface search via a Conformation Scanning method free energy calculations via free energy perturbation or weighted histogram analysis fitting of intermolecular potential parameters to structural and thermodynamic data global optimizing via energy surface smoothing including a Potential Smoothing and Search PSS methodAwards editTinker HP received the 2018 Atos Joseph Fourier Prize in High Performance Computing See also editList of software for Monte Carlo molecular modeling Comparison of software for molecular mechanics modeling Molecular dynamics Molecular geometry Molecular design software Comparison of force field implementationsReferences editLagardere Louis Jolly Luc Henri Lipparini Filippo Aviat Felix Stamm Benjamin Jing Zhifeng F Harger Matthew Torabifard Hedieh Cisneros Andres Schnieders Michael Gresh Nohad Maday Yvon Ren Pengyu Ponder Jay Piquemal Jean Philip 2018 Tinker HP Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi GPUs systems Chemical Science 9 4 956 972 doi 10 1039 C7SC04531J PMC 5909332 PMID 29732110 Adjoua Olivier Lagardere Louis Jolly Luc Henri Durocher Arnaud Wang Zhi Very Thibaut F Dupays Isabelle Jaffrelot Inizan Theo Celerse Frederic Ren Pengyu Ponder Jay Piquemal Jean Philip 2021 Tinker HP a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Journal of Chemical Theory and Computation 17 4 2034 2053 doi 10 1021 acs jctc 0c01164 PMC 7654869 PMID 33173801 Rackers Joshua A Wang Zhi Lu Chao Maury Marie L Lagardere Louis Schnieders Michael Piquemal Jean Philip Ren Pengyu Ponder Jay 2018 Tinker 8 Software Tools for Molecular Design Journal of Chemical Theory and Computation 14 10 5273 5289 doi 10 1021 acs jctc 8b00529 PMC 6335969 PMID 30176213 Harger Matthew Li Daniel Wang Zhi Dalby Kevin Lagardere Louis Piquemal Jean Philip Ponder Jay W Ren Pengyu 2017 Tinker OpenMM Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs Journal of Computational Chemistry 38 23 2047 2055 doi 10 1002 jcc 24853 PMC 5539969 PMID 28600826 Ren Pengyu Ponder Jay W 2003 Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation The Journal of Physical Chemistry B 107 24 5933 5947 doi 10 1021 jp027815 Pappu Rohit V Hart Reece K Ponder Jay W 1998 Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization The Journal of Physical Chemistry B 102 48 9725 CiteSeerX 10 1 1 18 1162 doi 10 1021 jp982255t Kong Yong Ponder Jay W 1997 Calculation of the reaction field due to off center point multipoles The Journal of Chemical Physics 107 2 481 Bibcode 1997JChPh 107 481K doi 10 1063 1 474409 Dudek Michael J Ponder Jay W 1995 Accurate modeling of the intramolecular electrostatic energy of proteins Journal of Computational Chemistry 16 7 791 CiteSeerX 10 1 1 502 6823 doi 10 1002 jcc 540160702 S2CID 15899639 Kundrot Craig E Ponder Jay W Richards Frederic M 1991 Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization Journal of Computational Chemistry 12 3 402 CiteSeerX 10 1 1 511 419 doi 10 1002 jcc 540120314 S2CID 53518520 Ponder Jay W Richards Frederic M 1987 An efficient newton like method for molecular mechanics energy minimization of large molecules Journal of Computational Chemistry 8 7 1016 doi 10 1002 jcc 540080710 S2CID 11607431 License edit Tinker licenseExternal links editTinkerTools on GitHub 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