TINKER

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. 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

Programs are provided to perform many functions including:
# energy minimization 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; and
# global optimization via energy surface smoothing including an own "Potential Smoothing and Search" (PSS) method.

ee also

* Molecular dynamics
* Molecular geometry

References

* P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation, J. Phys. Chem. B, 107, 5933-5947 (2003).
* R. V. Pappu, R. K. Hart and J. W. Ponder, Analysis and Application of Potential Energy Smoothing for Global Optimization, J. Phys. Chem. B, 102, 9725-9742 (1998).
* Y. Kong and J. W. Ponder, Reaction Field Methods for Off-Center Multipoles, J. Chem. Phys., 107, 481-492 (1997).
* M. J. Dudek and J. W. Ponder, Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins, J. Comput. Chem., 16, 791-816 (1995).
* C. E. Kundrot, J. W. Ponder and F. M. Richards, Algorithms for Calculating Excluded Volume and Its Derivatives as a Function of Molecular Conformation and Their Use in Energy Minimization, J. Comput. Chem., 12, 402-409 (1991).
* J. W. Ponder and F. M. Richards, An Efficient Newton-like Method for Molecular Mechanics Energy Minimization of Large Molecules, J. Comput. Chem., 8, 1016-1024 (1987).

External links

* [http://dasher.wustl.edu/tinker/ TINKER website]


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Synonyms:
(of old pans, kettles, etc.), (as old pans, kettles, etc.), , , , ,


Look at other dictionaries:

  • Tinker — bezeichnet: als Fremdbezeichnung die Mitglieder des Volks der Pavee eine Pferderasse, die von den Pavee verwendet wurde, siehe Tinker (Pferd) den Luftwaffenstützpunkt Tinker Air Force Base der US Air Force (USAF) in Oklahoma City (OK), USA in… …   Deutsch Wikipedia

  • tinker — ► NOUN 1) a travelling mender of pots, kettles, etc. 2) Brit., chiefly derogatory a gypsy or other person living in a travelling community. 3) Brit. informal a mischievous child. 4) an act of tinkering with something. ► VERB (tinker with) ▪… …   English terms dictionary

  • tinker — [tiŋ′kər] n. [ME tinkere < ? or akin to tinken, to make a tinkling sound] 1. a usually itinerant person who mends pots, pans, etc. 2. [sometimes T ] [Chiefly Irish & Scot.] Chiefly Irish Chiefly Scot. GYPSY (n. 1) 3. a person who can make all… …   English World dictionary

  • Tinker — Tink er, v. i. To busy one s self in mending old kettles, pans, etc.; to play the tinker; to be occupied with small mechanical works. [1913 Webster] …   The Collaborative International Dictionary of English

  • Tinker — Tink er, n. [From {Tink}, because the tinker s way of proclaiming his trade is to beat a kettle, or because in his work he makes a tinkling noise. Johnson.] 1. A mender of brass kettles, pans, and other metal ware. Tailors and tinkers. Piers… …   The Collaborative International Dictionary of English

  • TINKER — est un logiciel de simulation en dynamique moléculaire avec un paquet complet et général pour la mécanique moléculaire et des fonctions spéciales pour les biopolymères. Le cœur de TINKER est un ensemble modulaire de routines autorisant la… …   Wikipédia en Français

  • tinker — (n.) mender of kettles, pots, pans, etc., mid 13c. (as a surname), of uncertain origin. Some connect the word with the sound made by light hammering on metal. The verb meaning to keep busy in a useless way is first found 1650s. Tinker s damn… …   Etymology dictionary

  • Tinker — Tink er, v. t. [imp. & p. p. {Tinkered}; p. pr. & vb. n. {Tinkering}.] To mend or solder, as metal wares; hence, more generally, to mend. [1913 Webster] …   The Collaborative International Dictionary of English

  • tinker — index repair Burton s Legal Thesaurus. William C. Burton. 2006 …   Law dictionary

  • tinker — meaning ‘to play about’, is now normally followed by with rather than (as formerly) by at: • Whatever moral doubts there may be about tinkering with nature, the biotechnology revolution will not be stopped in its tracks Oxfam News, 1990 …   Modern English usage

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