Old Smoldyn versions
We have old versions of Smoldyn starting from 1.72; email email@example.com if you want one of them.
Example configuration files
S7_surfaces: absorb1.txt, absorb2.txt, absorb3.txt, cellmesh.txt, cellmeshfile.txt, diffuse2.txt, diffuse3.txt, jump1.txt, jump2.txt, jump3.txt, rafts.txt, reflect1.txt, reflect2.txt, reflect3.txt, stick2.txt, stickrate.txt, surf1.txt, surf2.txt, surf2react.txt, surf3.txt, surfrxn.txt, transmit1.txt, transmit2.txt, transmit3.txt, emitter1.txt, sphere.txt
S8_reactions: allostery.txt, allostery.tif, benchmark.txt, bireactAA.txt, bireactAB.txt, bireactABB.txt, bounce.tif, bounce.txt, crowding.tif, crowding.txt, confspread.tif, confspread.txt, equil.txt, lotvolt.tif, lotvolt.txt, lotvolt2.txt, lotvolt3.txt, unireact1.txt, unireactn.txt, wallreact.txt, zeroreact.txt
Published configuration files
To Smoldyn users: please help others build on your work by making any configuration files for research that you published available for others to use. Appropriate places for posting them are (1) in the supplementary information of your published paper, (2) on your webpage, and (3) here, on this webpage, by e-mailing them to us. We will happily archive any and all Smoldyn configuration files.
Andrews, Addy, Brent, Arkin, "Detailed simulations of cell biology with Smoldyn 2.1" PLoS Comp. Biol. 6:e1000705, 2010
Figure 1: ecoli.txt, hopdiffpos.txt, MoroneData.txt, spine.txt
Table 2: SuppA.pdf, bireactAB.txt, benchmark.txt
Figure 3: SuppB.pdf, diffi.txt, unireact1.txt, bireactABB.txt, stickrate.txt
Computational efficiency: SuppC.pdf, systemsize.txt
Bar1 model: SuppD.pdf, Bar29.txt, ellipse_12_12.txt