View source for Tinker (software)

{{about|a computer program for molecular dynamics||Tinker (disambiguation)}}
{{Infobox software
| name = Tinker
| logo = 
| screenshot = 
| caption = 
| collapsible = 
| author = Jay Ponder, Pengyu Ren, Jean-Philip Piquemal
| developer = 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]],
| released = {{Start date and age|1996|11|26}}
| latest release version = 8.10.2
| latest release date = {{Start date and age|2022|4|1}}
| latest preview version = 
| latest preview date = 
| programming language = [[Fortran 95]], [[CUDA]], [[OpenMP]] and [[Message Passing Interface|MPI Parallel]]
| operating system = [[Microsoft Windows|Windows]], [[macOS]], [[Linux]], [[Unix]]
| platform = 
| size = 
| language = English
| genre = [[Molecular dynamics]]
| license = [[Proprietary software|Proprietary]] [[freeware]]<ref>[http://dasher.wustl.edu/tinker/downloads/license.pdf Tinker license]</ref>
| website = {{URL|http://tinkertools.org}}
| frequently updated = 
}}
'''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.

Tinker works on [[Microsoft Windows|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 (programming language)|C]].

Core developers are: (a) [https://dasher.wustl.edu/ 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) [https://faculty.engr.utexas.edu/ren/home 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) [http://piquemalresearch.com/ 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==
The Tinker package is based on several related codes: (a) [https://dasher.wustl.edu/tinker the canonical Tinker], version 8, (b) the Tinker9 package as a direct extension of canonical Tinker to GPU systems, (c) [http://www.ip2ct.upmc.fr/tinkerHP the Tinker-HP package] for massively parallel MPI applications on hybrid [[CPus|CPU]] and [[GPUs|GPU-based systems]], (d) Tinker-FFE for visualization of Tinker calculations via a Java-based graphical interface, and (e) [http://biomol.bme.utexas.edu/tinker-openmm/index.php/Main_Page 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 coordinate system|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 ==
* Tinker-HP received the 2018 [https://globenewswire.com/news-release/2018/07/06/1534057/0/en/Atos-and-GENCI-announce-Winners-of-Atos-Joseph-Fourier-Award-2018.html Atos-Joseph Fourier Prize] in High Performance Computing.

== See also ==
* [[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]]

==References==
{{refbegin}}
* {{Cite journal|doi=10.1039/C7SC04531J|pmid=29732110|pmc=5909332|last1=Lagardère|first1=Louis|last2=Jolly|first2=Luc-Henri|last3=Lipparini|first3=Filippo|last4=Aviat|first4=Félix|last5=Stamm|first5=Benjamin|last6=Jing|first6=Zhifeng F.|last7=Harger|first7=Matthew|last8=Torabifard|first8=Hedieh|last9=Cisneros|first9=Andrés|last10=Schnieders|first10=Michael|last11=Gresh|first11=Nohad|last12=Maday|first12=Yvon|last13=Ren|first13=Pengyu|last14=Ponder|first14=Jay|last15=Piquemal|first15=Jean-Philip|title=Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. |journal=Chemical Science|year= 2018|volume=9 |pages=956–972   |issue=4}}
* {{Cite journal|doi=10.1021/acs.jctc.0c01164|pmid=33173801|pmc=7654869|last1=Adjoua|first1=Olivier|last2=Lagardère|first2=Louis|last3=Jolly|first3=Luc-Henri|last4=Durocher|first4=Arnaud|last5=Wang|first5=Zhi|last6=Very|first6=Thibaut F.|last7=Dupays|first7=Isabelle|last8=Jaffrelot Inizan|first8=Theo|last9=Célerse|first9=Frédéric|last10=Ren|first10=Pengyu|last11=Ponder|first11=Jay|last12=Piquemal|first12=Jean-Philip|title=Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields |journal=Journal of Chemical Theory and Computation|year= 2021|volume=17 |pages=2034–2053 |issue=4}}
* {{Cite journal|doi=10.1021/acs.jctc.8b00529|last1=Rackers|first1=Joshua A. | last2=Wang|first2=Zhi| last3=Lu | first3= Chao| first4=Marie L.|last4=Maury| last5=Lagardère|first5=Louis|last6=Schnieders|first6=Michael |first7=Jean-Philip | last7=Piquemal |last8=Ren|first8=Pengyu|last9=Ponder|first9=Jay|title= Tinker 8: Software Tools for Molecular Design |journal=Journal of Chemical Theory and Computation|year= 2018|volume=14 |pages=5273–5289 |issue=10|pmid=30176213 |pmc=6335969 }}
* {{Cite journal|doi=10.1002/jcc.24853|pmid=28600826|pmc=5539969|last1=Harger|first1=Matthew|last2=Li|first2=Daniel|last3=Wang|first3=Zhi|last4=Dalby|first4=Kevin|last5=Lagardère|first5=Louis| last6=Piquemal|first6=Jean-Philip|last7=Ponder|first7=Jay W.|last8=Ren|first8=Pengyu|title=Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs|journal=Journal of Computational Chemistry|year= 2017|volume= 38|pages= 2047–2055 |issue=23}}
* {{Cite journal|doi=10.1021/jp027815+|first1=Pengyu |last1=Ren |first2= Jay W. |last2=Ponder| title=Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation|journal=The Journal of Physical Chemistry B|year= 2003|volume= 107|pages= 5933–5947 |issue=24}}
* {{Cite journal|doi=10.1021/jp982255t|title=Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization|year=1998|last1=Pappu|first1=Rohit V.|last2=Hart|first2=Reece K.|last3=Ponder|first3=Jay W.|journal=The Journal of Physical Chemistry B|volume=102|issue=48|pages=9725 |citeseerx=10.1.1.18.1162}}
* {{Cite journal|doi=10.1063/1.474409|title=Calculation of the reaction field due to off-center point multipoles|year=1997|last1=Kong|first1=Yong|last2=Ponder|first2=Jay W.|journal=The Journal of Chemical Physics|volume=107|issue=2|pages=481|bibcode = 1997JChPh.107..481K |doi-access=free}}
* {{Cite journal|doi=10.1002/jcc.540160702|title=Accurate modeling of the intramolecular electrostatic energy of proteins|year=1995|last1=Dudek|first1=Michael J.|last2=Ponder|first2=Jay W.|journal=Journal of Computational Chemistry|volume=16|issue=7|pages=791|citeseerx=10.1.1.502.6823|s2cid=15899639 }}
* {{Cite journal|doi=10.1002/jcc.540120314|title=Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization|year=1991|last1=Kundrot|first1=Craig E.|last2=Ponder|first2=Jay W.|last3=Richards|first3=Frederic M.|journal=Journal of Computational Chemistry|volume=12|issue=3|pages=402 |citeseerx=10.1.1.511.419|s2cid=53518520 }}
* {{Cite journal|doi=10.1002/jcc.540080710|title=An efficient newton-like method for molecular mechanics energy minimization of large molecules|year=1987|last1=Ponder|first1=Jay W.|last2=Richards|first2=Frederic M.|journal=Journal of Computational Chemistry|volume=8|issue=7|pages=1016|s2cid=11607431 }}
{{refend}}

==License==
{{Reflist}}

==External links==
* {{GitHub|TinkerTools}}
* {{Twitter|TINKERtoolsMD}}
* {{URL|https://tinkertools.org}}
* {{URL|https://dasher.wustl.edu/tinker}}

{{DEFAULTSORT:Tinker}}
[[Category:Science software]]
[[Category:Molecular dynamics software]]
[[Category:Monte Carlo molecular modelling software]]
[[Category:Washington University in St. Louis]]