www.neuron.yale.edu

Continuing the discussion-- I did not implement this model, so regard everything that follows as informed speculation. What was the purpose of this particular model? Presumably to use the phenomenon of spatial summation to illustrate certain features of NEURON. This required a cellular topology that...

How did you decide the values for the membrane mechanisms and morphology? The same way that one would design a computational model of any other physical system. First determine the purpose of the model, which is usually to study some phenomenon of interest that occurs in a physical system. Then dec...

Two recommendations. 1. For the reasons mentioned above, don't activate the synapse at 0 ms. Instead, let the model execute for at least 1 ms before activating the synapse. 2. Use an FInitializeHandler (default type is good for this) to do two things during model initialization: (1) set the SEClamp'...

I am simulating a neural dynamic when it receives a synaptic input at t=0. An important concern in any experiment, whether on a living cell or a computational model, is the initial state of the system (cell or model) before any stimulus or perturbation is applied. If it is not in a resting state at...

I already know the mechanism: with a short pulse, there isn’t enough time for the membrane to depolarize and reach the activation threshold. True, but that's easily overcome by increasing stimulus amplitude, and it's only half of the story. A longer duration extracellular pulse can (1) reduce excit...

in DBS, which the pulses are short, the high frequency is important to the AP generation. Stimulus pulse duration is important, but you'll never guess why unless you take the time to learn more about the mechanistic basis of cellular excitability. And that should be covered in a good introductory c...

It is the rare EE major that has much reading, classroom, or hand-on exposure to neurophysiology, and in particular practical aspects of stimulating excitable tissue (nerve, muscle). That's something you'll have to correct sooner or later if you plan to work at the interface between engineering and ...

By setting a pulse duration of 100 ms, I see AP generation. However, if I reduce the pulse width to 0.1 ms, APs are not generated. Is this expected behavior

To help guide my answer, it would be useful to know if your background is primarily in physics/math/engineering, or in biology.

First thing to check: what are the anatomical and biophysical properties of your model cell? What does
somaL.psection()
tell you? and how about somaR.psection()?

Could it be Linux is not GUI based ?? I think you'd know by now if the OS and hardware on the machine on which you're running NEURON have GUI support. Are you executing NEURON on a laptop or desktop machine, or on some remote server? Assuming NOT the latter, what happens if you execute neurondemo i...

Instead of matplotlib and pyplot, try plotly.

Oops, instead of replying to a copy of your original post, I edited it, inserting my replies. How careless of me; done when I was hurrying to get to the point but not cautious about how it was done. But at least I didn't destroy your questions, and perhaps my replies will be helpful to you and others.

This example of how to develop and use a Linear Circuit implementation of a gap junction via Python https://www.neuron.yale.edu/ftp/ted/neu ... cirgap.zip might provide some useful hints.

Interesting. Needs to be brought to the attention of the NEURON development team. Regarding what you should do, if your goal is to do science, decide what's most important to you--cosmetics, or results; spending time trying to work around problems in development code, or addressing scientific proble...

Sure, if you want to rewrite those statements in Python, go ahead. Here's a seed to get you started. I have even corrected the comment in the second statement.