Tinker (software)

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This article is about a computer program for molecular dynamics. For other meanings of Tinker, see Tinker (disambiguation).
Tinker
Developer(s) Jay Ponder
Written in FORTRAN77
Operating system Windows, Mac, and Unix/Linux
Type Molecular dynamics
License Proprietary freeware[1]
Website dasher.wustl.edu/tinker/

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 heart of the Tinker package is a modular set of callable routines which allow the manipulation of coordinates and evaluation of potential energy and derivatives in a straightforward fashion.

Tinker works on Windows, Mac, and Unix/Linux and its source code is available free of charge under a restrictive license. The code was written in FORTRAN77 with common extensions and some C. The code is maintained by Jay Ponder at the Washington University School of Medicine.

Features[edit]

Programs are provided to perform many functions including:

  1. energy minimization 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; and
  13. global optimization via energy surface smoothing, including a "Potential Smoothing and Search" (PSS) method.

See also[edit]

References[edit]

  • 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. 

References[edit]

External links[edit]