This is the readme for the mcell simulation associated with the paper Keller D, Babai N, Kochubey O, Han Y, Markram H, Schürmann F, Schneggenburger R (2015) An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse. PLoS Comput Biol 11:e1004253 The directory is organized into supporting subsolders and main simulations. The supporting subfolders are: data_files : data waveforms used for driving reaction rates molecules : the base molecules used in the simulations rates : the rates used by the reactions geometry_files : geometry of the system mechanisms : reactions that the molecules undergo parameters : common parameters used by the simulation There are four main simulations in the following directories: small_AZ_random small_AZ_exclusion small_AZ_exclusion_EGTA large_AZ_exclusion Each of these contains a subfolder with an mcell_top.mdl and variables.mdl file. The main file is mcell_top.mdl and variables contains variables particular to that simulation. To run the simulation, change to the subdirectory/1.0 and execute: mcell mcell_top.mdl In general, many seeds must be run due to the stochasticity of the simulation. Questions can be addressed to: daniel.keller@epfl.ch