CPU Dasher

The Tinker molecular modeling software is a complete and generalpackage for molecular mechanics and dynamics, with some special featuresfor biopolymers. Tinker has the ability to use any of several commonparameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM(19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA,OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizablemodel, AMOEBA (2004, 2009, 2013, 2017, 2018) polarizable atomic multipoleforce fields, AMOEBA+ that adds charge penetration effects, and our newHIPPO (Hydrogen-like Interatomic Polarizable POtential) force field.Parameter sets for other force field models are under consideration forfuture releases.

The Tinker software contains a variety of interesting algorithmssuch as: flexible implementation of atomic multipole-based electrostaticswith explicit dipole polarizability, various continuum solvation treatmentsincluding several generalized Born (GB/SA) models, generalized Kirkwoodimplicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmanncalculations, efficient truncated Newton (TNCG) local optimization,surface areas and volumes with derivatives, free energy calculations viathe Bennett Acceptance Ratio (BAR) method, normal mode vibrational analysis,minimization in Cartesian, torsional or rigid body space, symplectic RESPAmultiple time step integration for molecular dynamics, velocity Verletstochastic dynamics, pairwise neighbor lists and splined spherical energycutoff methods, particle mesh Ewald (PME) summation for partial charges andpolarizable multipoles, a novel reaction field treatment of long rangeelectrostatics, fast distance geometry metrization with better samplingthan standard methods, Elber's reaction path algorithm, potentialsmoothing and search (PSS) methods for global optimization, Monte CarloMinimization (MCM) for efficient potential surface scanning, tools forfitting charge, multipole and polarization models to QM-based electrostaticpotentials and more....

Tinker 8 is a major new release of the Ponder Lab tool set formolecular mechanics and dynamics calculations. An important change inthis new version is the switch from old-style common blocks to Fortranmodules. Use of modules and greatly increased use of dynamic memoryallocation means Tinker can now support very large molecular systems.Tinker 8 also implements improved OpenMP parallelization throughoutmany parts of the code. Additional major improvements include parallelneighbor list building and updating, and big reduction in iterationneeded to converge polarization via an efficient PCG solver.

Other changes from the previous Tinker version include new and updatedforce field parameter sets and numerous minor additions and bug fixes,many of them suggested by users of the package. Please note that as withprior new releases, version 8 is neither backward nor forward compatiblewith earlier versions of Tinker. In particular, older versions of parameterfiles should not be used with Tinker 8 executables and vice versa.

While we strongly suggest users switch to Tinker 8 with its manyimportant new features and bug fixes, we provide download links below forprior stable versions, Tinker 7.1.3, Tinker 6.3.3, Tinker 5.1.9 andTinker 4.3. Tinker 6 and later is OpenMP parallel and written in Fortran 95,while Tinker 4 and 5 are in serial, extended Fortran 77.

This distribution version of Tinker, with full source code, is licensedfree of charge to academic research groups, government laboratories, andnon-profit organizations. Use in commercial settings requires a commerciallicense, as described in the Tinker License Agreement found below.

Download links are provided in the bottom section of this web page. Majornew releases of the package with additional features are generally placedon this site during February, June and October. Minor changes and bug fixesare added to the distribution version as we finish testing them. The basicpackage has been used by the Ponder lab and others at WashingtonUniversity for several years and should be fairly robust. All we askis that you notify us of any bugs, features you would like to seeimplemented, or major code extensions that you add yourself.

Non-commercial users who make significant use of the package shouldcomplete and return by regular post or email the license form availablebelow. The forms are used to aid us in convincing colleagues Tinker isused outside of Washington University, which helps us justify furtherdevelopment of the programs. We try to respond to email as time allows.Comments are always welcome and should be directed to Jay Ponder atponder@dasher.wustl.edu.

Tinker is also available on Github! The TinkerTools organization has a fullGithub site at https://github.com/TinkerTools with complete source codefor canonical Tinker and other packages in the Tinker software suite. Themaster repository on the Github site is updated frequently with new minorfeatures and bug fixes. It the place to go for the latest revisions of thesoftware. Prebuilt executables are not available via the Github site.

Tinker 8 is provided as a complete source distribution via the links below.After unpacking the distribution, you can build a set of Tinker executableson almost any machine with a Fortran compiler. Makefiles, a GNU autoconfconfigure script, as well as standalone scripts to compile, build objectlibraries, and link executables on a wide variety of machine-CPU-operatingsystem combinations are provided.

If you wish to build the OpenMP-capable parallel version of Tinker, objectlibraries from the FFTW 3.3 Fourier transform package are required. The FFTWlibraries must be available in the one of the locations searched by theTinker Makefile prior to building Tinker executables. Optional Support forAPBS Poisson-Boltzmann calculations within Tinker requires object librariesfrom the APBS 1.3 software package.

Pre-built Tinker executables for Linux, macOS, and Windows are also availablefor download below. They should run on most recent vintage machines usingthe above operating systems, and can handle a maximum of 1 million atomsprovided sufficient memory is available. The Linux executables require atleast glibc-2.6 or later. Note starting with Tinker 8, we no longer providepre-built executables for 32-bit operating systems.

The provided executables are OpenMP capable, but do not support APBSor the Tinker-FFE interface. You will still need to have a copy of thecomplete Tinker distribution as it contains the parameter sets, examples,benchmarks, test files and documentation required to use the package.

Only a very few portions of Tinker still make use of static memoryallocation, however some of the executables can require a large memory(i.e., total of actual RAM and swap space/virtual memory) to handlelarge molecular systems. There are instructions available on the internet forincreasing the size of the swap space/virtual memory under various versionsof Linux and Windows. If a program fails with the message 'insufficientvirtual memory', 'resource temporarily unavailable' or a 'segmentationfault', then you may need to add swap space. macOS increases the sizeof the swap space automatically as needed, and such modifications are notneeded to use Tinker on a Macintosh.

Force Field Explorer (Tinker-FFE) is a Java-based GUI for the Tinker package.It provides visualization for Tinker molecule files, as well as launching ofTinker calculations from a graphical interface. The original version of FFEwas written by Michael Schnieders, now on the Biomedical Engineering facultyat the University of Iowa, prior to and during his thesis work in St. Louis.It was further revised by Jeff Bigg, Tyler Ponder and Brendan McMorrow duringsummers spent in the Ponder lab. A major update for Tinker 8, renamedTinker-FFE, was completed in July 2017. Tinker-FFE for Linux, MacOS andWindows can be downloaded from the lower section of this web page as'installation kits' containing the FFE GUI and an FFE-enabled version ofTinker. Tinker-FFE requires a 64-bit CPU and operating system, as 32-bitsystems are no longer supported.

Integration with Tinker, including the ability to interactively run Tinkercalculations, and to access molecule downloads from the PubChem, NCI and PDBdatabases make Tinker-FFE a useful tool in classroom teaching environments.For research work, we recommend using the latest command line version ofTinker for numerical calculations, and using FFE or another visualizationprogram to view results. Several other visualization programs (including VMD,Avogadro, Jmol, MOLDEN, WebMO, some PyMOL versions, etc.) can displayTinker structure and MD trajectory files.

For those wishing to modify the FFE GUI or build a version from source,we provide a complete development package for Tinker-FFE. This is a largedownload which contains the code for all components, including the Java sourcefor FFE itself and the many required Java libraries. This package allowsbuilding Tinker-FFE on all three supported operating systems from a commoncode base. External requirements are the GNU compiler suite with gcc, g++ andgfortran (on Windows use the MinGW-w64 GNU compilers under Cygwin), and theInstall4j Multi-Platform Java Installer Builder.

Installation Notes for Tinker-FFE on Linux:

The Tinker-FFE Installer for Linux is provided as a gzipped shell script.Uncompress the the .gz archive to produce an .sh script, and then runthe script. The script must have the 'executable' attribute, set via'chmod +x *.sh', prior to being run. If you have the installer generate adesktop icon, you may need to make the icon 'launchable'. This is done onUbuntu by right clicking on the icon and selecting 'Allow Launching'.

On some older Linux distributions, the Tinker-FFE Installer does not launchcorrectly or hangs. For these systems, we provide an alternative Tinker-FFEdistribution as a gzipped tar archive. Download this Tinker-FFE archive,ungzip the file and copy it to the end user's home directory, then extractthe distribution there via the 'tar xvf' command. The application is locatedin $HOME/Tinker-FFE/ffe/.

Installation Notes for Tinker-FFE on macOS:

The Tinker-FFE Installer for macOS is provided as a .dmg disk image file.Double-click on the file to run the installer. Recent versions of macOScontain a security feature called Gatekeeper that keeps applications notobtained via the App Store or Apple-approved developers from being opened.Gatekeeper is enabled by default, and may result in the (incorrect!) errormessage: 'Tinker-FFE Installer.app is damaged and can't be opened.'To turn off Gatekeeper, go to the panel System Preferences > Security &Privacy > General, and set 'Allow apps downloaded from:' to 'Anywhere'. Thiswill require an Administrator account, and must be done before invoking theFFE installer. Once FFE is installed and launched for the first time, youcan return the System Preference to its prior value. On macOS 10.12 andlater, the 'Anywhere' option has been removed. In most cases the Security& Privacy panel will open and permit the user to run the installer. Alternatively, the 'Anywhere' option can be restored by running the command'sudo spctl --master-disable' in a Terminal window.

Installation Notes for Tinker-FFE on Windows:

The Tinker-FFE Installer for Windows is provided as a zipped executable.First, unzip the .zip file, then run the resulting executable .exe file.In order to perform minimizations or molecular dynamics from within FFE,some environment variables and symbolic links must be set prior to usingthe program. A batch file named 'FFESetupWin.bat' is installed in themain Tinker-FFE directory, which by default resides in the user's homedirectory. To complete the setup of FFE, this batch file should be runfrom a Command Prompt window following installation. It is only necessaryto invoke this batch file once, as the settings should persist betweenlogins.

OpenMM is a molecular modeling library developed at Stanford University.It supports the AMOEBA force field, and supplies CUDA code implementing AMOEBAon NVIDIA GPUs. On this site we provide code interfacing selected Tinkerprograms with OpenMM. The source code and a Makefile needed to constructOpenMM-enabled Tinker ANALYZE, BAR and DYNAMIC programs is available belowfor download. The Makefile assumes OpenMM 7.1 or later is installed and aCUDA-capable graphics card is present. Depending upon the size of the systembeing simulated and the GPU card available, OpenMM-based Tinker moleculardynamics is very significantly faster than the standard CPU-based version.

To build Tinker-OpenMM executables, you must have an NVIDIA GPU installedon your build system along with the CUDA development environment includingthe 'nvcc' CUDA compiler. Download and install the current OpenMM versionfrom Github. Then follow the instructions in the /openmm directory of thefull Tinker distribution, or use the equivalent Tinker interface code forOpenMM for provided as a separate download below. Tinker-OpenMM executableshave been tested on Linux, and should also work under Windows. Due to theregretable disfunction between Apple and NVIDIA, the last version of MacOSwith available NVIDIA graphics drivers is 10.13.6 (High Sierra), the lastversion of CUDA to work with macOS is CUDA 10.2, and only GPU cards throughthe GeForce GTX 10 ('Pascal') series are supported.

Tinker is available on the Google Play Store for a variety of Android devicesvia self-extracting installers implemented and maintained by Alan Liska andVeronika Ruzickova of the J. Heyrovksy Institute of Physical Chemistry inPrague. Binaries and documentation are also available from the MobileChemistry Portal located at http://www.jh-inst.cas.cz/~liska/Tinker.htm/.

We have big plans for the Tinker package going forward. New program packagesin the Tinker family, Tinker 9 and Tinker-HP, are under active development.Our future development will focus on free energy calculations, major newsampling methods, enhanced crystal modeling capability, improved force fieldparameterization methods, additions to the AMOEBA model, and new force fields,including AMOEBA+ and HIPPO.

Tinker 9 is a reimplementation of significant portions of Tinker in C++,using OpenACC and CUDA to support NVIDIA GPU calculations. Tinker-HP is andistributed, MPI-parallel Fortran code that is also GPU capable via use ofCUDA for compute intensive functions. Both of these Tinker-based codes areavailable from the TinkerTools Github site. Suggestions and commentsregarding possible additions to Tinker or other codes in the Tinker familyare always welcome. Of course, offers to provide or help write code are evenbetter....

Tinker Summary Sheet

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Tinker License Agreement

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Tinker Wiki Site

WEBSITE

Tinker User's Guide

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Tinker Logo Illustration

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Tinker Distribution Directory

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Force Field Parameter Sets

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Tinker Source Code Directory

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Tinker Package Distribution (GZIP, 69.5 Mb)

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Tinker Package Distribution (ZIP, 77.9 Mb)

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Tinker Executables for Linux (GZIP, 89.2 Mb)

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Tinker Executables for macOS (GZIP, 90.9 Mb)

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Tinker Executables for Windows (ZIP, 97.8 Mb)

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Tinker Validation Suite for MMFF (GZIP, 5.68 Mb)

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Tinker Interface Code for OpenMM (GZIP, 61.7 Kb)

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Previous Release of Tinker 7.1.3 (GZIP, 28.7 Mb)

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Previous Release of Tinker 6.3.3 (GZIP, 20.5 Mb)

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Previous Release of Tinker 5.1.9 (GZIP, 14.1 Mb)

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Previous Release of Tinker 4.3 (GZIP, 7.5 Mb)

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Tinker-FFE (Force Field Explorer) User's Guide

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Tinker-FFE Installer for Linux (GZIP SH, 343.6 Mb)

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Tinker-FFE Distribution for Linux (GZIP TAR, 332.1 Mb)

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Tinker-FFE Installer for macOS (DMG, 285.8 Mb)

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Tinker-FFE Installer for Windows (ZIP, 278.9 Mb)

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Force Field Explorer Development Kit (GZIP, 1.39 Gb)

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Tinker's 'Molecular Mechanics' Logo Illustration by Jay Nelson.Courtesy of Prof. Robert Paine, Chemistry Department, University ofNew Mexico.

Installation kits for Force Field Explorer (FFE) are built using theInstall4j Multi-Platform Java Installer Builder from ej-technologies GmbH.

Early development of Tinker was supported by Awards DBI 9808317,MCB 0344670 and CHE 0535675 from the National Science Foundation, andNIH Grant R01 GM58712 from the United States National Institutes of Health.Recent funding of the Tinker software and AMOEBA polarizable forcehas been provided by NSF Awards CHE 1152823 and CHE 1265731, and by NIHGrants R01 GM106137 and R01 GM 114237.

Any opinions, findings, and conclusions or recommendations expressedin the Tinker Molecular Modeling package are those of the authors and donot reflect the views of either the National Science Foundation or theNational Institutes of Health.