Download Smoldyn

Current version:

2.51

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 2.51:

Platforms

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

Old versions

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

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 (SmoldynUsersManual.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:

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.

Support

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 rest of the code is Copyright 2003-2016 by Steven Andrews and also distributed under the Gnu LGPL. Contact us if you would like Smoldyn to use a different license.

Revision History