Download Smoldyn

Current version:

2.15

Download Package

Download Smoldyn 2.15: Smoldyn-2.15.tar.gz or Smoldyn-2.15.zip

This download includes the source code, documentation, makefiles, test files, binaries, wrl2smol, and SmolCrowd utilities. It compiles on Macintosh and Linux with the GNU build system and it includes executable applications for Windows.

Platforms

Most Mac, Linux, or Windows computers up to about 5 years old should run Smoldyn. Some addition software is required as well though. If it isn't already installed on your computer, get it here. Full installation instructions, for this software and for Smoldyn, are given in the Smoldyn Users' Manual.

• Mac: get gcc at http://connect.apple.com/
• Mac or Linux: get libtiff at http://www.libtiff.org/
• Windows: necessary dll files should be in Smoldyn download; if not, try http://www.dlldump.com/

Documentation

The Smoldyn manual is in two parts. Part I (Smoldyn_doc1.pdf) is the Smoldyn User's Manual and Part II (in the download package) is the Smoldyn Programmer's Manual. Also, in the documentation directory of the download, you will find the libmoleculizer manual for rule-based reaction network generation, and programmers' documentation for all of Smoldyn's libraries. 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
• Lok and Brent, 2005 - rule-based modeling

Support

• Try the user's forum
• E-mail Steve at support@smoldyn.org

Bugs

No significant bugs are known for the core Smoldyn program, although we are still working to fix several minor ones. Some new features (multiple threads, reaction network generation, and mid-simulation system modifications) have several bugs that we're still working on. Known bugs are listed at end of part II of the documentation. If you have a configuration file that causes crashes or incorrect behavior (even if you find a work-around), please send it to us at support@smoldyn.org so we can find the bugs.

News

Version 2.1 has substantially improved graphics from prior versions. These additions are not documented well yet, but the basics are described in the reference section of the manual. Check out the "graphics opengl_better" and "light" statements.

More recent version include several small updates. Versions 2.11 and 2.12 include minor improvements to the build system and a few new commands. Version 2.13 includes better reaction detail reporting and some libmoleculizer improvements. Version 2.14 had bugs in it. Version 2.15 fixed those bugs and a bug that occured on Windows, and is better with "continuation reactions", such as A -> B+C and B+C -> D.

License

The rxnparam.c and SurfaceParam.c source code files are in the public domain. The libmoleculizer module is Copyright 2009 by the Molecular Sciences Institute and distributed under the Gnu General Public License (GPL). The rest of the code is Copyright 2003-2010 by Steven Andrews and distributed under the Gnu GPL (it was LGPL up to version 2.04). Contact us if you would like Smoldyn to use a different license.

Revision History

• 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.