Download Smoldyn

Current version:

2.73

Download Packages

All downloads include the documentation, examples, utility software, and necessary install scripts. See the included README file for installation advice. If the advice there isn't sufficient, then check the Smoldyn User's Manual or send an e-mail for support. The complete distributions are for users who need to compile their own code; they compile on Macintosh and Linux and should also compile on Windows with a little effort.

Packages for version 2.73:

• smoldyn-2.73-mac-Intel.tgz - Pre-compiled software for Intel Macs with OS 10.9 or higher.
• smoldyn-2.73-mac.tgz - Pre-compiled software for Apple Silicon Macs with OS 12 or higher.
• smoldyn-2.73-windows.zip - Pre-compiled software for Windows; supports hybrid simulation but not VTK visualization. No tiff support; see below.
• smoldyn-2.73.tgz - Complete distribution with source code, no pre-compiled code. CMake build system.
• smoldyn-2.73.zip - Complete distribution with source code, no pre-compiled code. CMake build system.

Platforms

Most Mac, Linux, or Windows computers up to about 5 years old should run Smoldyn. See below for detailed advice.

• Mac: Check what kind of Mac you have by clicking on the Apple menu and selecting "About This Mac"; the chip/processor will be either Intel or Apple. Run Smoldyn with the Terminal application (Applications/Utilities/Terminal). Install with the included script by typing "sudo ./install.sh" and then entering your password. If you're compiling your own code, get XCode at https://developer.apple.com/xcode/ and libtiff at http://www.libtiff.org/.
• Linux: Dilawar Singh compiled Smoldyn for several Linux flavors, all of which are at https://software.opensuse.org//download.html?project=home%3Adilawar&package=smoldyn. If you're compiling your own code, you may need to download some widely used libraries, which are libtiff, zlib, and freeglut. Depending on your system, you can probably download them with the apt-get or yum package managers. Be sure to get the developer versions (e.g. libtiff-devel), because they come with header files, which are necessary.
• Windows: Run Smoldyn with the Command Prompt application (Start > All Programs > Windows System > Command Prompt). Install with the included script by running "install.bat" as administrator. You should not need dll files, but if you do, check the Smoldyn download; alternatively, try getting them at http://www.dlldump.com/. Put dll files in the same directory as the Smoldyn executable. If your system doesn't automatically recognize your dll files, then open a command prompt, running it as system administrator, change to the SysWOW64 folder or wherever the dll file is, and enter, for example, "regsvr32.exe freeglut.dll".

Repository

The master Smoldyn repository is at github at https://github.com/ssandrews/Smoldyn. If you would like to help develop Smoldyn, please let me know and I'll be happy to get you started.

Old versions

The latest version is usually the best choice, but users occasionally ask for old versions. If you want an old version, send an e-mail to me and I'll put it here.

• smoldyn-2.48.tgz

Documentation

For a quick introduction to Smoldyn, look at the two-page quick reference guide, SmoldynQuickGuide.pdf. The Smoldyn manual is much more thorough and is in two parts. Part I (SmoldynManual.pdf) is the Smoldyn User's Manual and Part II (in the download package) is the Smoldyn Programmer's Manual. Although less comprehensive, this Methods for Molecular Biology paper provides an easy-to-read introduction to Smoldyn. It also gives lots of modeling suggestions that are not listed elsewhere, such as about time steps and parameter values. The documentation directory of the download includes programmers' documentation for all of Smoldyn's libraries and additional documentation.

Most of the Smoldyn algorithms are described in the papers:

• Andrews and Bray, 2004 - diffusion and reaction algorithms
• Andrews, 2005 - physical justification for binding and unbinding radii
• Andrews, 2009 - molecule-surface interaction algorithms
• Robinson et al., 2015 - Hybrid simulation methods

GPU Smoldyn

Two groups independently parallelized portions of Smoldyn to run on NVIDIA Graphics Processing Units (GPUs), producing about 200x (!) faster simulations. These Smoldyn versions are written in the CUDA language. In general, they support Smoldyn's core functionality but not most of Smoldyn's features. I have not compiled or run these versions myself yet.

• Lorenzo Dematté's version - available here or at github. This version, created as part of Lorenzo's PhD research, only supports reactions and diffusion. It does not use Smoldyn's configuration file input language. I think this version is more quantitatively accurate than the Gladkov version (it performs reactions on reactant pairs where the two molecules are in different virtual boxes).
• Denis Gladkov's version - available here. This version, created in Roshan D'Souza's laboratory, supports reactions, diffusion, and reflective interactions with triangle-composed surfaces. It includes compiling instructions and mostly supports standard Smoldyn configuration files. Tests suggest that this version may be about 20% faster than the Dematté version.

Support

• E-mail Steve Andrews at support@smoldyn.org

Bugs

Although I work very hard to prevent bugs in Smoldyn, it is under active development, so it undoubtedly includes some bugs. If you have a configuration file that causes crashes or incorrect behavior (even if you find a work-around), please send it to me at support@smoldyn.org so I can find the bugs.

License

The rxnparam.c and SurfaceParam.c source code files are in the public domain. The Next Subvolume module is Copyright 2012 by Martin Robinson and is distributed under the Gnu LGPL license. The Python binding code is Copyright 2020-2021 by Dilawar Singh and is distributed under the Gnu GPL v. 3 license. The rest of the code is Copyright 2003-2021 by Steven Andrews and also distributed under the Gnu LGPL. Contact me if you would like Smoldyn to use a different license.

Revision History

• 2.73 (2/27/24) - Fixed bug in setreactionratemolcount, changed default 'bounce' reaction to overlap method, and added PYTHON_VERSION to compile options.
• 2.72 (8/17/23) - Accurate diffusion at locations where the coefficient changes, better tiff timing, improved command line options, now logging file option, fixed bug in excluded volume reactions, longer string lengths.
• 2.71 (2/6/23) - Added translatemol command for advection simulations. Also fixed minor bugs with Python API.
• 2.70 (10/25/22) - Exposed reaction probability entry to Libsmoldyn and Python APIs
• 2.69 (10/17/22) - Fixed minor bugs in commands run through Python interface.
• 2.68 (7/19/22) - Added listmolssurf command. Also native support for Apple Silicon M1 chip.
• 2.67 (11/2/21) - Fixed bug in longrangeforce command. Also updates to Biosimulators code.
• 2.66 (6/18/21) - Fixed documentation formatting, added Biosimulators links, preliminary filament support.
• 2.65 (5/19/21) - Python API improvements and added longrangeforce command.
• 2.64 (3/24/21) - Fixed minor bugs with reactions on surfaces, converted user's manual to LaTeX, and merged Libsmoldyn manual with regular manual.
• 2.63 (12/15/20) - Improved Python bindings, added Python example files, and fixed bug with moving surfaces.
• 2.62 (10/14/20) - Added Python bindings, improved Windows build now with MSVC, subtantial build system refactoring.
• 2.61 (7/22/19) - Minor bug fixes: improved radialdistfunction and surface detection near system boundaries.
• 2.60 (6/7/19) - Smoldyn really works on Windows. Also, some minor bug fixes.
• 2.59 (5/15/19) - Major progress in getting Smoldyn to work on Windows again.
• 2.58 (3/29/19) - Improved math precision, improved single-molecule tracking, fixed bug in probabilistic commands (e.g. killmolprob), enabled command probability to depend on molecule location.
• 2.57 (3/21/19) - Math supports scientific notation, allowed species change with surface actions, improved single-molecule tracking. Smoldyn is now on github.
• 2.56 (9/18/18) - Got MinGW compiling to work again for Windows. Fixed minor bugs. Largely completed lambda-rho reaction algorithm support, although some minor calculation errors remain.
• 2.55 (7/16/18) - Several minor bug fixes. This version was not compiled for Windows due to compiler problems.
• 2.54 (8/27/17) - Fixed minor bug that affected drift of surface-bound molecules.
• 2.53 (5/25/17) - Fixed minor bugs that arose when counting molecules during hybrid simulations and fixed errors that arose with certain compilers.
• 2.52 (5/16/17) - Fixed very minor bug that arose when counting molecules during hybrid simulations.
• 2.51 (3/15/17) - Fixed trivial bug that caused compiling errors and bug that affected surface-interactions of surface-bound molecules.
• 2.50 (2/28/17) - Improved support for moving surfaces and developed infrastructure for state-observation functions.
• 2.49 (2/17/17) - Added partial support for moving surfaces and for the use of basic math functions in input files.
• 2.48 (11/16/16) - Fixed a few minor bugs which caused crashes in unusual situations.
• 2.47 (8/30/16) - Improved rule-based modeling with wildcards with fixed bugs, rules for molecular properties, and properties for reaction rules.
• 2.46 (7/30/16) - Rule-based modeling with wildcards is now true on-the-fly, expanding only as needed.
• 2.45 (7/15/16) - Fixed several minor bugs, including in equilmol command, math parsing, and hybrid simulations.
• 2.44 (6/27/16) - Simplified input of reverse reactions and returned freeglut.dll to the windows download.
• 2.43 (5/18/16) - Improved Libsmoldyn compiling and linking, renamed documentation, and added some commands.
• 2.42 (4/29/16) - Fixed minor bugs. Excluded volume reactions now work well and added overlapping space hybrid simulation.
• 2.41 (4/8/16) - Fixed several bugs that arose in v. 2.40, added tutorial section to User's Manual, and improved algorithm for excluded volume reactions.
• 2.40 (3/22/16) - Lots of new features: rule-based modeling with BioNetGen, rule-based modeling with wildcards, variables and arithmetic in input files, fixed several more bugs in surface diffusion, several new commands.
• 2.39 (1/15/16) - Fixed another important bug in surface diffusion. Quantitatively validated results. Accelerated virtual box assignment, which especially helps when molecules are unevenly distributed.
• 2.38 (10/22/15) - Lots of minor bug fixes and feature additions. New features: fixmolcountrange commands, quit_at_end statement, reaction_intersurface statement, more versatile bounce and confspread reactions, works on older Mac systems.
• 2.37 (10/7/15) - Fixed a major bug that affected diffusion of surface-bound molecules. In the process, sped up surface-bound diffusion. Also added support for single molecule tracking with serial number control and reaction logging.
• 2.36 (6/9/15) - Fixed a minor bug that affected some bounce type reactions.
• 2.35 (4/23/15) - Fixed a bug that led to incorrect reaction rates for some first order reactions. The affected ones are those in which a single reactant can react via multiple first order reactions and reaction probabilities are high.
• 2.34 (1/8/15) - Made the lattice code part of the pre-compiled distribution and nearly finished BNG parsing.
• 2.33 (10/9/14) - Fixed several small bugs and added a few example files (e.g. MinD oscillation).
• 2.32 (8/29/14) - Added adjacent-volume hybrid simulation with NSV module, improved wildcard support, enabled molecule clustering simulations, added VTK visualization, and removed Libmoleculizer and threading support
• 2.31 (9/9/13) - Fixed a minor bug in meansqrdisp3 command and added setreactionratemolcount command.
• 2.30 (8/21/13) - Fixed some very minor bugs and added several runtime commands.
• 2.29 (4/10/13) - Small improvements to Libmoleculizer and a few minor bug fixes.
• 2.28 (8/29/12) - Improved CMake build system and fixed a few minor bugs. Added rudimentary filament code.
• 2.27 (7/26/12) - Added molecular drift relative to surface coordinates and settable precision for numerical output. Improved simulation of molecules with excluded volume so rebound is not to fixed distance but equals prior overlap. Also, changed code from C to C++, changed build system from AutoTools to CMake, improved internal error handling, and coordinated development with VCell team.
• 2.26 (3/2/12) - Finished rule-based modeling with Libmoleculizer, added partial wildcard support, and enabled excluded volume reactions with periodic boundaries.
• 2.25 (9/26/11) - Fixed minor bugs and improved Ubuntu installation.
• 2.24 (7/27/11) - Major work on Libsmoldyn to the point that it's fairly complete and it seems to work. Also, major work on the build system, which enabled the distribution of pre-compiled code. Finally, of course, fixed some minor bugs and added a few commands.
• 2.23 (6/24/11) - Added preliminary Libsmoldyn API, made all memory allocation dynamic, added molecule list and reaction list shuffling, added display of time and molecule counts to graphics window, added several commands, improved mid-simulation modifications, and fixed several minor bugs.
• 2.22 (3/22/11) - Fixed a bug that prevented compiling when OpenGL was disabled. Also added a skeleton for libsmoldyn.
• 2.21 (3/11/11) - Fixed minor bugs that affected surface-bound molecule diffusion and surface detection.
• 2.20 (3/4/11) - Fixed major bug with non-threading installations (including the Windows version), improved define statements, and modified configure defaults.
• 2.19 (2/11/11) - Surface-bound molecules can interact with other surfaces, added --define command line option, added append_files statement, added ifincmpt and killmolincmpt commands, and cleaned up surface code.
• 2.18 (1/6/11) - Fixed bug that affected desorbed molecules.
• 2.17 (11/19/10) - Improved Ubuntu installation and fixed a bug for partially transmitting surfaces with large transmission coefficients.
• 2.16 (9/24/10) - Fixed bug that affected desorbed molecules.
• 2.15 (7/20/10) - Fixed bugs that were introduced with version 2.14.
• 2.14 (7/18/10) - Fixed integer command queue for Windows and improved continuation reactions.
• 2.13 (7/15/10) - Better reaction detail reporting and improved libmoleculizer operation.
• 2.12 (6/10/10) - Added commands: molcountincmpts and replacecmptmol.
• 2.11 (5/4/10) - Slight improvement to build system.
• 2.10 (3/24/10) - Major code improvement on libmoleculizer module.
• 2.09 (1/6/10) - Substantially improved graphics and added movesurfacemol and molcountincmpt2 commands.
• 2.08 (11/20/09) - Released unofficially. This fixed a few minor bugs.
• 2.07 (11/17/09) - Fixed bugs. In particular, fixed diffusion of surface-bound molecules.
• 2.06 (11/6/09) - Molecules can change species at surfaces and surface-bound molecules jump at "jump" surfaces. Also, bug fixes and general code cleanup.
• 2.05 (7/23/09) - Nathan got the build system to work well for most Mac and Linux systems. Some documentation updates.
• 2.04 (6/27/09) - Debugged and improved build system and support for multimeric complexes, although they still lack complete documentation. Also added support for effectve unbounded diffusion.
• 2.03 (5/22/09) - Changed from a make file build to the GNU build system (autoconf, automake, etc.), added support for multimeric complexes and for multiple program threads. These new features are unstable.
• 2.02 (5/5/09) - Added a few commands, cleaned up some code, and fixed a few bugs.
• 2.01 (3/3/09) - Improved diffusion of surface-bound molecules and simplified block-style input formats.
• 2.0 (2/17/09) - Fixed a few trivial bugs, and increased the version number to 2.0.
• 1.89 (2/11/09) - Adsorption, desorption, and partial transmission algorithms now work well and have been verified to be accurate. Also added molecules with excluded volume. Lots of new code structure improvements will enable several planned features (including macromolecular complexes and a command line user input).
• 1.88 (1/16/09) - First release of SmolCrowd utility program, adsorption, desorption and partial transmission should be correct but have not been verified, improved integer-time commands, and simplified the configuration file format slightly.
• 1.87 (12/7/08) - Vastly improved the wrl2smol utility program.
• 1.86 (11/17/08) - Fixed several minor bugs, improved makefiles for more reliable installation, and made Smoldyn compatible with 64-bit machines.
• 1.85 (6/3/08) - The Mersenne Twister is now used for random numbers, added define statements to parser, renamed allosteric reactions to conformational spread reactions, and fixed lots of minor bugs and one significant one (reaction products ended up across surfaces).
• 1.84 (4/11/08) - First Windows release. Also, added reactions that are only active in specified compartments, added several commands, and fixed the change time step command.
• 1.83 (3/14/08) - Improved unimolecular reaction rates for multiple reaction channels, improved allosteric reactions, and added molecular drift.
• 1.82 (2/28/08) - Fixed a bug in which reaction products ended up across surfaces. Also, reactions were completely overhauled and can now be entered with a vastly improved format. Allosteric reactions were added.
• 1.81 (1/23/08) - Surface-bound molecules now work, lots of minor bugs were fixed, multiple molecule lists were implemented, porting works well, and documentation was improved.
• v1.80 (12/22/07) - 'Q' now quits the program, time steps can be changed mid-simulation, and basic porting between Smoldyn and MOOSE was added.
• v1.79 (12/6/07) - Fixed more bugs with commands. Also added basic compartments.
• 1.78 (11/30/07) - Fixed lots of bugs with surface-bound molecules and commands, and improved input formats of several statements.
• 1.77 (11/18/07) - Fixed a few minor bugs and modified several functions to make Smoldyn easier to parallelize.
• 1.76 (11/7/07) - Main source file was split to two files and assorted function rearranging. More command-line options are now available.
• 1.75 (11/6/07) - Added support of surface-bound molecules, which still need some debugging. Also, changed several surface input statement formats. The documentation is current, but incomplete.
• 1.74 (10/22/07) - Fixed yet more bugs in surfaces, added disk-shaped surface panels, and made some changes in surface input statement formats. Only the code got updated for this release, so the documentation is slightly out of date.
• 1.73 (9/25/07) - Minor surface improvements, added exponential time-stepping option for run-time commands, and improved multi-platform compiling.
• 1.72 (2/26/07) - Surfaces are finally totally functional for both diffusion and reactions (or so I thought for a while).
• 1.71 (12/8/06) - Better surface support with cylinder and hemisphere panels, and improved reflective surfaces.
• 1.70 (5/17/06) - Reasonably good surface support, where surfaces can be reflective, absorbing or transparent, and they are comprised of panels that can be rectangular, triangular, or spherical.
• 1.59 (?) - Displays the random number seed.
• 1.58 (7/22/05) - A new runtime command, a randomized Brownian dynamics lookup table to remove artifacts that can arise from random number generator problems, and a more versitile mol statement.
• 1.57 (2/17/05) - A new runtime command.
• 1.56 (1/14/05) - Improved graphics and a few other minor changes.
• 1.55 (8/20/04) - Minor graphics changes, some improvements in the design of the command queue for the runtime command interpreter, and it is now possible for commands to return error messages.
• 1.53 (2/9/04) - Cleaned up code for the runtime command interpreter, it is now possible to save file stacks, minor display and user interface improvements, and several new commands for text output and excluded volumes.
• 1.52 (10/24/03) - A significant bug was fixed in the equation for absorbing walls (thanks to Dan Gillespie for catching it), it is now possible to pause simulations while using graphics, and a few minor bugs were fixed.
• 1.51 (9/5/03) - Unimolecular reactions can now have much lower reaction rates, a memory error upon termination was fixed, parameter checking was improved, several minor bugs were fixed, and two new interpreter commands were added.
• 1.5 (7/2003) - First public release.