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 Pierre and Marie Curie University
Initial release September 8, 2004 (2004-09-08)
Stable release
8.1.2 / February 17, 2017 (2017-02-17)
Development status Active
Written in Fortran 95, OpenMP Parallel
Operating system Windows, OS X, Linux, Unix
Available in English
Type Molecular dynamics
License Proprietary freeware[1]
Website dasher.wustl.edu/tinker

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 manipulaing 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 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 Pierre and Marie Curie 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.X, https://dasher.wustl.edu/tinker); ii) the Tinker-OpenMM package (http://biomol.bme.utexas.edu/tinker-openmm/index.php/Main_Page) for Tinker's use with GPus; iii) the Tinker-HP package (http://www.ip2ct.upmc.fr/tinkerHP) for massively parallel MPI applications on CPus and Xeon Phi .

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

References

  1. ↑ Tinker license
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