Tinker (software)

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	FORTRAN 77
Operating system	Windows, OS X; Unix, Linux
Type	Molecular dynamics
License	Proprietary freeware
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 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, Mac, and Unix-Linux and its source code is available free of charge under a restrictive license. The code was written in FORTRAN 77 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:

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

• List of software for Monte Carlo molecular modeling
• List of software for molecular mechanics modeling
• Molecular dynamics
• Molecular geometry
• Molecular design software
• Force field implementation
• Folding@home

External links

• Official website