TINKER is a computer software

Computer software

Computer software, or just software, is a collection of computer programs and related data that provide the instructions for telling a computer what to do and how to do it....

 application for molecular dynamics

Molecular dynamics

Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...

 simulation with a complete and general package for molecular mechanics

Molecular mechanics

Molecular mechanics uses Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields...

 and molecular dynamics

Molecular dynamics

Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...

, with some special features for biopolymer

Biopolymer

Biopolymers are polymers produced by living organisms. Since they are polymers, Biopolymers contain monomeric units that are covalently bonded to form larger structures. There are three main classes of biopolymers based on the differing monomeric units used and the structure of the biopolymer formed...

s. 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

C (programming language)

C is a general-purpose computer programming language developed between 1969 and 1973 by Dennis Ritchie at the Bell Telephone Laboratories for use with the Unix operating system....

. The code is maintained by Jay Ponder at the Washington University School of Medicine

Washington University School of Medicine

Washington University School of Medicine , located in St. Louis, Missouri, is one of the graduate schools of Washington University in St. Louis. One of the top medical schools in the United States, it is currently ranked 4th for research according to U.S. News and World Report and has been listed...

.

Features

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
   Simulated annealing
   Simulated annealing is a generic probabilistic metaheuristic for the global optimization problem of locating a good approximation to the global optimum of a given function in a large search space. It is often used when the search space is discrete...
   
    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
    Free energy perturbation
    Free energy perturbation theory is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations. The FEP method was introduced by R. W. Zwanzig in 1954...
    
     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

• List of software for Monte Carlo molecular modeling
• Molecular dynamics
  Molecular dynamics
  Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
  
  
• Molecular geometry
  Molecular geometry
  Molecular geometry or molecular structure is the three-dimensional arrangement of the atoms that constitute a molecule. It determines several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism, and biological activity.- Molecular geometry determination...
  
  
• Molecular design software
  Molecular Design software
  Molecular design software is software for molecular modeling, that provides special support for developing molecular models de novo.In contrast to the usual molecular modeling programs such as the molecular dynamics and quantum chemistry programs, such software directly supports the aspects related...
  
  
• Force field implementation
  Force field implementation
  This is a table of computer programs implementing molecular mechanics force fields.-See also:*Force field *List of software for Monte Carlo molecular modeling*Molecular mechanics*Molecular design software*Molecule editor...
  
  
• Folding@Home
  Folding@home
  Folding@home is a distributed computing project designed to use spare processing power on personal computers to perform simulations of disease-relevant protein folding and other molecular dynamics, and to improve on the methods of doing so...