Tinker, previously stylized as TINKER, is a suite of computer software applications for molecular dynamics simulation. The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics, with some special features for biomolecules. The core of the software is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means.
| Original author(s) | Jay Ponder, Pengyu Ren, Jean-Philip Piquemal |
|---|---|
| Developer(s) | Jay Ponder Lab, Department of Chemistry, Washington University in St. Louis; Pengyu Ren Lab, Department of Biomedical Engineering, the University of Texas at Austin; Jean-Philip Piquemal, Sorbonne University, |
| Initial release | November 26, 1996 |
| Stable release | 8.10.2
/ April 1, 2022 |
| Written in | Fortran 95, CUDA, OpenMP and MPI Parallel |
| Operating system | Windows, macOS, Linux, Unix |
| Available in | English |
| Type | Molecular dynamics |
| License | Proprietary freeware[1] |
| Website | tinkertools |
Tinker works on Windows, macOS, Linux and Unix. The source code is available free of charge to non-commercial users under a proprietary license. The code is written in portable FORTRAN 77, Fortran 95 or CUDA with common extensions, and some C.
Core developers are: (a) the Jay Ponder lab, at the Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri. Laboratory head Ponder is Full Professor of Chemistry, and of Biochemistry & Molecular Biophysics; (b) the Pengyu Ren lab , at the Department of Biomedical Engineering University of Texas in Austin, Austin, Texas. Laboratory head Ren is Full Professor of Biomedical Engineering; (c) Jean-Philip Piquemal's research team at Laboratoire de Chimie Théorique, Department of Chemistry, Sorbonne University, Paris, France. Research team head Piquemal is Full Professor of Theoretical Chemistry.
Features edit
The Tinker package is based on several related codes: (a) the canonical Tinker, version 8, (b) the Tinker9 package as a direct extension of canonical Tinker to GPU systems, (c) the Tinker-HP package for massively parallel MPI applications on hybrid CPU and GPU-based systems, (d) Tinker-FFE for visualization of Tinker calculations via a Java-based graphical interface, and (e) the Tinker-OpenMM package for Tinker's use with GPUs via an interface for the OpenMM software. All of the Tinker codes are available from the TinkerTools organization site on GitHub. Additional information is available from the TinkerTools community web site.
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
Awards edit
- Tinker-HP received the 2018 Atos-Joseph Fourier Prize in High Performance Computing.
See also edit
References edit
- Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F.; Harger, Matthew; Torabifard, Hedieh; Cisneros, Andrés; Schnieders, Michael; Gresh, Nohad; Maday, Yvon; Ren, Pengyu; Ponder, Jay; Piquemal, Jean-Philip (2018). "Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems". Chemical Science. 9 (4): 956–972. doi:10.1039/C7SC04531J. PMC 5909332. PMID 29732110.
- Adjoua, Olivier; Lagardère, Louis; Jolly, Luc-Henri; Durocher, Arnaud; Wang, Zhi; Very, Thibaut F.; Dupays, Isabelle; Jaffrelot Inizan, Theo; Célerse, Frédéric; Ren, Pengyu; Ponder, Jay; Piquemal, Jean-Philip (2021). "Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields". Journal of Chemical Theory and Computation. 17 (4): 2034–2053. doi:10.1021/acs.jctc.0c01164. PMC 7654869. PMID 33173801.
- Rackers, Joshua A.; Wang, Zhi; Lu, Chao; Maury, Marie L.; Lagardère, Louis; Schnieders, Michael; Piquemal, Jean-Philip; Ren, Pengyu; Ponder, Jay (2018). "Tinker 8: Software Tools for Molecular Design". Journal of Chemical Theory and Computation. 14 (10): 5273–5289. doi:10.1021/acs.jctc.8b00529. PMC 6335969. PMID 30176213.
- Harger, Matthew; Li, Daniel; Wang, Zhi; Dalby, Kevin; Lagardère, Louis; Piquemal, Jean-Philip; Ponder, Jay W.; Ren, Pengyu (2017). "Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs". Journal of Computational Chemistry. 38 (23): 2047–2055. doi:10.1002/jcc.24853. PMC 5539969. PMID 28600826.
- 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. CiteSeerX 10.1.1.18.1162. 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. CiteSeerX 10.1.1.502.6823. doi:10.1002/jcc.540160702. S2CID 15899639.
- 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. CiteSeerX 10.1.1.511.419. doi:10.1002/jcc.540120314. S2CID 53518520.
- 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. S2CID 11607431.