These are supplement files for the NEURON model used in my PLoSCB 2017 manuscript.
To run the model, type nrngui in commandline to run the NEURON simulator. Type in or copy paste the command from main.hoc line by line. So you can visualize the voltage from soma section.

All ion conductance parameters are in params.txt. See the file params.notes for what each parameter represents.
The pyramidal cell morphology can be retrieved from n400td-pc2-sp-axn.hoc.
The directory ca1n1-mod contains all .mod files for ion channels, including various Na+ channels, K+ channels, Ca2+ channels, and so on. The x86_64 folder contains all those compiled mod files for Unix 64bit OS. The synaptic release mechansim is coded in expsyn2c.mod.

Synaptic release is probabilistic, following a probability profile measured in an electrophysiology experiment study. The probability is stored in the file relpr_smooth_col4.dat.

There are in 190 spines in total. Synapse release patterns can be adjusted using the function syn_set_col4() in syn.hoc file. The parameters for the function are the total number of synaptic stimulation, the number of stimulations in each action potential bursts (for Theta burst), number of AMPARs in each spine, number of NMDARs, the short interval between synapstic stimulation within a burst (in ms), and the long interval between consecutive groups of bursts (in ms). As an example, these parameter values can be 150, 5 200, 10, 10, 250, respectively, which generats an equvalent of 4 Hz Theta bursts stimulations.