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If you actually have a copy of The NEURON Book , see the discussion in 9.10.1 Modeling diffusion with kinetic schemes . Any reader of this thread who does not have the book may download this earlier draft of chapter 9 https://www.neuron.yale.edu/ftp/ted/book/revisions/chap9indexedref.pdf and read Mo...

Not related to the problem that triggered this thread, but something you need to know: for your ODE-described calcium accumulation mechanism, use derivimplicit rather than cnexp. See Integration methods for SOLVE statements https://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592 in the Hot tips a...

If it is absolutely essential to place "something" at a very particular location along a neurite, then represent the neurite by two sections connected in series, assign each section whatever length you need, and place the "something" at their junction point. Then you are free to use whatever values ...

If a section.parentseg().x = 0.5 and parent_section.n3d = 21, does that mean that section is connected to parent_section somewhere around the 10th-11th 3d xyz point? No. Reflect on the fact that what governs the placement of xyzdiam measurements along the length of an unbranched neurite are the irr...

On Linux it generates a folder x86_64 . . . The documentation mentions that nrn_load_dll works for Linux, but I don't see a dll file? The file you want to load is x86_64/.libs/libnrnmech.so You realize that, by doing this, you are writing code that will not work under MSWin or MacOS. And unless you...

Thanks, that will be a useful tip for others who may read this thread.

Your post actually contains signs of multiple problems. I'm using the Import3D tool on a .asc file. I'm then using the n3d, x3d, y3d, and z3d functions on a section to iterate over what I presume are the 3D positions of all the segments in that section You realize that * a section's first and last 3...

Check to see if the readline library exists on your computer. If it doesn't, download and install it, then uninstall and reinstall NEURON. How? Depends on your Linux distribution. For distributions that use rpm for package management, rpm -q readline and rpm -ivh readline are your friends. Debian-re...

For hypothesis testing purposes I'd like to have one compartment in the multi-compartment cell transmitting currents to all the connected compartments but not receiving current from all compartments. Is that doable in NEURON? If I correctly understand what you want (and I'm assuming that you aren't...

I'm distributing models as part of a python package. During a post-install script I'd like to compile all of the mod files that are in a subfolder of the package, and I'd like NEURON to be able to find the resulting .dll from any folder on that machine. Right now it only seems to look in the curren...

I'm trying to obtain the surface of the different compartments. I understood that to obtain it for a section I should write totalarea_soma = 0 soma for (x,0) totalarea_soma += area(x) # take into account the number of nseg True. soma for (x,0) statement is equivalent to the following pseudocode: fo...

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See chapter 9 of the NEURON Book. If you don't have the book, get this preprint https://www.neuron.yale.edu/ftp/ted/book/revisions/chap9indexedref.pdf If you installed NEURON from source code, see nrn/share/examples/nrniv/nmodl/cadif.mod which may be slightly different from the example in the book. ...

That's a very good question. NEURON's computational engine can calculate ionic equilibrium potentials in the course of a simulation. If your model includes an NMODL-specified "ion accumulation mechanism" (a mechanism with a USEION statement that WRITEs the intra- or extracellular concentration of on...

No, NEURON works with Python 2.7 as well. But there's not much point in configuring NEURON to use 2.7 because the people who develop Python are terminating support for 2.7 in 2020. If I were you, I'd uninstall both NEURON and Python, then I'd install the latest stable Python 3.x, and after that I'd ...