Tinker Molecular Modeling


Tinker - Software Tools for Molecular Design

Current Major Version: Tinker 8.4

Release Date: February 2018

Minor Version: 8.4.4 (May 1, 2018)


Introduction

    The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Tinker has the ability to use any of several common parameter 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 polarizable model, and the AMOEBA (2004, 2009, 2013, 2017, 2018) polarizable atomic multipole force field. Parameter sets for other widely-used force fields are under consideration for future releases.

    The Tinker software contains a variety of interesting algorithms such as: flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, free energy calculations via the Bennett Acceptance Ratio (BAR) method, normal mode vibrational analysis, minimization in Cartesian, torsional or rigid body space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling than standard methods, Elber's reaction path algorithm, potential smoothing and search (PSS) methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, tools for fitting charge, multipole and polarization models to QM-based electrostatic potentials and more....

Current Release

    Tinker 8 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. An important change in this new version is the switch from old-style common blocks to Fortran modules. Use of modules and greatly increased use of dynamic memory allocation means Tinker can now support very large molecular systems. Tinker 8 also implements improved OpenMP parallelization throughout many parts of the code. Additional big improvements include parallel neighbor list building and updating, and big reduction in iteration needed to converge AMOEBA polarization via an efficient PCG solver. Other changes from the previous Tinker version include new and updated force field parameter sets and numerous minor additions and bug fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 8 is neither backward nor forward compatible with earlier versions of Tinker. In particular, older versions of parameter files should not be used with Tinker 8 executables and vice versa.

    While we strongly suggest users switch to Tinker 8 with its many important new features and bug fixes, we provide download links below for prior stable versions, Tinker 7.1.3, Tinker 6.3.3, Tinker 5.1.9 and Tinker 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.

Availability

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

    Download links are provided in the bottom section of this web page. Major new releases of the package with additional features are generally placed on this site during February, June and October. Minor changes and bug fixes are added to the distribution version as we finish testing them. The basic package has been used by the Ponder lab and others at Washington University for several years and should be fairly robust. All we ask is that you notify us of any bugs, features you would like to see implemented, or major code extensions that you add yourself.

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

Installation

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

    If you wish to build the OpenMP-capable parallel version of Tinker, object libraries from the FFTW 3.3 Fourier transform package are required. Support for APBS Poisson-Boltzmann calculations within Tinker requires object libraries from the APBS 1.3 software package.

    Pre-built Tinker executables for Linux, MacOS, and Windows are also available for download below. They should run on most recent vintage machines using the above operating systems, and can handle a maximum of 1 million atoms provided sufficient memory is available. The Linux executables require at least glibc-2.6 or later. Note starting with Tinker 8, we no longer provide pre-built executables for 32-bit operating systems.

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

    Only a very few portions of Tinker still make use of static memory allocation, however some of the executables can require a large memory (i.e., total of actual RAM and swap space/virtual memory) to handle large molecular systems. There are instructions available on the internet for increasing the size of the swap space/virtual memory under various versions of Linux and Windows. If a program fails with the message "insufficient virtual memory", "resource temporarily unavailable" or a "segmentation fault", then you may need to add swap space. MacOS increases the size of the swap space automatically as needed, and such modifications are not needed to use Tinker on a Macintosh.

Force Field Explorer

    Force Field Explorer (FFE) is a Java-based GUI for the Tinker package. It provides visualization for Tinker molecule files, as well as launching of Tinker calculations from a graphical interface. The original version of FFE was written by Michael Schnieders, now on the Biomedical Engineering faculty at 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 during summers spent in the Ponder lab. A major update for Tinker 8 was completed in July 2017. FFE for Linux, MacOS and Windows can be downloaded from the lower section of this web page as "installation kits" containing the FFE GUI and an FFE-enabled version of Tinker. FFE requires a 64-bit CPU and operating system, as 32-bit systems are no longer supported.

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

    For those wishing to modify FFE or build their own version from source, we provide a complete development package for FFE. This is a large download which contains the code for all components, including the Java source for FFE itself and the many required Java libraries. This package allows building FFE on all three supported operating systems from a common code base. External requirements are the GNU compiler suite with gcc, g++ and gfortran (on Windows use MinGW-w64 compilers under Cygwin), and the Install4j Java installer builder. Note Install4j is a commercial product; only the compiler is needed, not the full Install4j GUI interface.

    Installation Notes for FFE on Linux:

    The FFE Installer for Linux is provided as a gzipped shell script. Uncompress the the .gz archive to produce an .sh script, and then run the script. The script must have the "executable" attribute, set via "chmod +x *.sh", prior to being run.

    Installation Notes for FFE on Macintosh:

    The FFE Installer for MacOS is provided as a .dmg disk image file. Double-click on the file to run the installer. MacOS 10.8 and later contains a security feature called Gatekeeper that keeps applications not obtained via the App Store or Apple-identified developers from being opened. Gatekeeper is enabled by default, and will result in the (incorrect!) error message: "Molecular Tools 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". This will require an Administrator account, and must be done before invoking the FFE installer. Once FFE is installed and launched for the first time, you can return the System Preference to its prior value. On Sierra (10.12) and later, the "Anywhere" option has been removed. The option can be restored by running the command "sudo spctl --master-disable" in a Terminal window.

    Installation Notes for FFE on Windows:

    The 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 using the program. A batch file named "FFESetupWin.bat" is installed with FFE in the MolecularTools directory, which by default resides in the user's home directory. To complete the setup of FFE, this batch file should be run from a Command Prompt window following installation. It is only necessary to invoke this batch file once, as the settings should persist between logins.

OpenMM Support

    OpenMM is a molecular modeling library developed at Stanford University. It supports the AMOEBA force field, and supplies CUDA code implementing AMOEBA on NVIDIA GPUs. On this site we provide code interfacing the Tinker molecular dynamics program with OpenMM. The source code and Makefile needed to build an OpenMM-enabled Tinker DYNAMIC executable is available below for download. The Makefile assumes OpenMM 7.1 or later is installed and a CUDA-capable graphics card is present. Depending upon the size of the system being simulated and the type of GPU card available, OpenMM-based Tinker molecular dynamics runs up to 20 times faster than the standard CPU-based version.

Future Development

    We have big plans for the Tinker package going forward. The next version of Tinker is already in the early design stage, and will include additional programs and features for free energy calculations, major new sampling methods, enhanced crystal modeling capability, more and better tools for force field parameterization, and some anticipated new energy components to enhance the accuracy and generality of AMOEBA. The existing work to augment Tinker for use on GPU-based systems via OpenMM, and under MPI parallelization via Tinker-HP will continue. Suggestions and comments regarding other possible additions to Tinker are always welcome. Of course, offers to provide or help write code are even better....


Tinker Downloads

Tinker Summary Sheet

PDF

Tinker License Agreement

PDF

Tinker Wiki Site

WEB SITE

Tinker User's Guide

PDF

Tinker Logo Illustration

GIF

Tinker Distribution Directory

DIRECTORY

Force Field Parameter Sets

DIRECTORY

Tinker Source Code Directory

DIRECTORY

Tinker Complete Distribution (GZIP, 35.5 Mb)

DOWNLOAD

Tinker Complete Distribution (ZIP, 37.8 Mb)

DOWNLOAD

Tinker Executables for 64-bit Linux (GZIP, 66.0 Mb)

DOWNLOAD

Tinker Executables for MacOS (GZIP, 69.8 Mb)

DOWNLOAD

Tinker Executables for 64-bit Windows (ZIP, 71.4 Mb)

DOWNLOAD

Validation Suite for MMFF in Tinker (GZIP, 5.7 Mb)

DOWNLOAD

Tinker Interface Code for OpenMM (GZIP, 58.1 Kb)

DOWNLOAD

Previous Release of Tinker 7.1.3 (GZIP, 28.7 Mb)

DOWNLOAD

Previous Release of Tinker 6.3.3 (GZIP, 20.5 Mb)

DOWNLOAD

Previous Release of Tinker 5.1.9 (GZIP, 14.1 Mb)

DOWNLOAD

Previous Release of Tinker 4.3 (GZIP, 7.5 Mb)

DOWNLOAD

Force Field Explorer User's Guide

PDF

Force Field Explorer for 64-bit Linux (GZIP, 267.6 Mb)

DOWNLOAD

Force Field Explorer for MacOS (DMG, 262.4 Mb)

DOWNLOAD

Force Field Explorer for 64-bit Windows (ZIP, 220.4 Mb)

DOWNLOAD

Force Field Explorer Development Kit (GZIP, 1.19 Gb)

DOWNLOAD




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

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

    Any opinions, findings, and conclusions or recommendations expressed in the Tinker Molecular Modeling package are those of the authors and do not reflect the views of either the National Science Foundation or the National Institutes of Health.



Last Update: May 1, 2018
Maintainer: ponder@dasher.wustl.edu (sendmail)