Old Smoldyn versions

We have old versions of Smoldyn starting from 1.72; email support@smoldyn.org if you want one of them.

Example configuration files

S1_intro: bounce1.txt, bounce2.txt, bounce3.txt

S2_config: config.txt, configcolors.txt, configmolecs.txt, define.txt, definecolors.txt, definemolecs.txt, ifdefine.txt

S3_space: bounds1.txt, bounds2.txt

S4_molecules: diffa.txt, diffa.tif, drift.txt, diffi.tif, diffi.txt, molecule.txt, mollist.txt

S5_graphics: better.txt, graphics1.txt, graphics2.txt, graphics3.txt

S6_commands: addspecies.txt, cmdfile.txt, cmdmanipulate.txt, cmdmovesurfacemol.txt, cmdobserve.txt, cmdtime1.txt, cmdtime2.txt, meansqrdisp2.txt

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

S9_compartments: compart.tif, compart.txt, compartlogic.tif, compartlogic.txt, compartrxn.txt

S10_boxes: box.txt, systemsize.txt

S11_ports: port.txt

S12_moleculizer: allostery.txt, allreceptor.txt, binding.txt, cmdtrial.txt, modifications.txt, oligo.txt, omniReceptor.txt, receptor-on-surface.txt, smallmol.txt, transformation-reactions.txt

S98_utilityprograms: out2D50.txt, sample-surface.wrl.txt, sample.txt, sphere.txt, spherebot.wrl.txt, spheretop.wrl.txt, tetrahedron.txt, tetrahedron.wrl.txt

S99_more: crowd.txt, crwd2D60.txt, neuron.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

published paper: Andrews_Arkin_2010.pdf
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

Dushek, van der Merwe, Shahrezaei, "Ultrasensitivity in Multisite Phosphorylation of Membrane-Anchored Proteins" Biophys. J. 100:1189-1197, 2011

simulation file: Dushek_Shahrezaei_2011_Smoldyn.txt

Hoffmann and Schwarz, "Oscillations of Min-proteins in micropatterned environments: a three-dimensional particle-based stochastic simulation approach" Soft Matter 10:2388, 2014

simulation file: smoldyn_script_Fig3.txt