|Original author(s)||Jay Ponder|
|Developer(s)||Jay Ponder Lab, Department of Chemistry, Washington University in St. Louis|
|Initial release||September 8, 2004|
7.1 / May 12, 2015
|Written in||FORTRAN 77|
|Operating system||Windows, OS X, Linux, Unix|
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.
Development occurs at the Jay Ponder Lab, at the Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri. Laboratory head Ponder is professor of chemistry (main appointment), biochemistry and molecular biophysics, and biomedical engineering.
Programs are provided to perform many functions including:
- energy minimizing 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
- global optimizing via energy surface smoothing, including a Potential Smoothing and Search (PSS) method
- List of software for Monte Carlo molecular modeling
- Comparison of software for molecular mechanics modeling
- Molecular dynamics
- Molecular geometry
- Molecular design software
- Comparison of force field implementations
- 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.