Tinker (software)

Tinker
Original author(s) Jay Ponder, Pengyu Ren, Jean-Philip Piquemal
Developer(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 Université,
Initial release September 8, 2004 (2004-09-08)
Stable release
8.1.2 / February 17, 2017 (2017-02-17)
Written in Fortran 95, CUDA, OpenMP and MPI Parallel
Operating system Windows, OS X, Linux, Unix
Available in English
Type Molecular dynamics
License Proprietary freeware[1]
Website tinkertools.org

Tinker, stylized as TINKER, is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for biopolymers. The core of the package is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means.

Tinker works on Windows, OS X, Linux and Unix. The source code is available free of charge under a restrictive license. The code is written in portable FORTRAN 77, FORTRAN 95 or CUDA with common extensions, and some C.

Core developers are: 1) 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 (main appointment), Biochemistry and Molecular Biophysics, and Biomedical Engineering; 2) 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; 3) Jean-Philip Piquemal's research team at Laboratoire de Chimie Théorique, Department of Chemistry, Sorbonne University, Paris. Research team head Piquemal is Full Professor of Theoretical Chemistry.

Features

The Tinker package is based on 3 codes: i) the canonical Tinker (version 8.); ii) the Tinker-OpenMM package for Tinker's use with GPus; iii) the Tinker-HP package for massively parallel MPI applications on CPus and Xeon Phi . Tinker-HP received the 2018 Atos-Joseph Fourier Prize in High Performance Computing.

Programs are provided to perform many functions including:

  1. energy minimizing over Cartesian coordinates, torsional angles, or rigid bodies via conjugate gradient, variable metric or a truncated Newton method
  2. molecular, stochastic, and rigid body dynamics with periodic boundaries and control of temperature and pressure
  3. normal mode vibrational analysis
  4. distance geometry including an efficient random pairwise metrization
  5. building protein and nucleic acid structures from sequence
  6. simulated annealing with various cooling protocols
  7. analysis and breakdown of single point potential energies
  8. verification of analytical derivatives of standard and user defined potentials
  9. location of a transition state between two minima
  10. full energy surface search via a Conformation Scanning method
  11. free energy calculations via free energy perturbation or weighted histogram analysis
  12. fitting of intermolecular potential parameters to structural and thermodynamic data
  13. global optimizing via energy surface smoothing, including a Potential Smoothing and Search (PSS) method

See also

References

  • 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: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields". Chemical Science. 9: 956–972. doi:10.1039/C7SC04531J.
  • 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.
  • 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. 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. doi:10.1002/jcc.540160702.
  • 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. doi:10.1002/jcc.540120314.
  • 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.

License

  1. ↑ Tinker license
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