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I think I resolved the issue. The problem seems to be that I first defined a "master" RxD region 'cyt' and then for each of the sections (already included in 'cyt') a separate miniregion cyts , and maybe that's what caused the error message "Rates and Reactions with species defined on...

I'm trying to introduce RxD species and reactions into a set of compartments in a multicompartmental neuron model and give inputs to some of the species. I have a list of sections for which I'm creating the Rxd Region (after defining a cell model L5PC, in this case a regular Hay model) as seclist = ...

I'm trying to make a .mod ion-channel mechanism file where the maximal conductance of the channel would depend on the concentration of a certain species. Currently all my molecular species are part of a list, meaning that they are called 'specs[0]' ... 'specs[19]' and I define my reactions as e.g. r...

I've got another issue related to this topic. I used to run my simulator from the command line (even inside a python script) to make sure there are no issues with reinitialization of the RxD model. Now I'm trying to rewrite the code to be run as a normal python function to avoid i/o overload on the ...

How to implement a decay reaction (a reaction with no products)?

In an earlier NEURON version it was possible to write
but now (v. 7.7) I get an error "AttributeError: 'Reaction' object has no attribute '_react_regions'"

Thanks for the reply. However, the problem persists even if I remove "nrn_region='i'", or change it to None or 'o'.

I get a weird "Abort trap: 6" error that seems to depend on the length of the names of my species. MWE: from neuron import h, rxd from pylab import * h.load_file('stdrun.hoc') dend = h.Section(name='dend') cyt = rxd.Region([dend], name='cyt', nrn_region='i') specNameLen=21 specs = [] vecs ...

I'm getting a syntax error with NEURON 7.5 whenever I try to assign something to diam3d(j), e.g.
forall {
for (j = 0; j < n3d(); j+=1) {
diam3d(j)=1.0
}
}

I have a reconstructed morphology (loaded from an .asc file), where I would like to change the diameters of the sections by some factor. Is there a neat way of doing it? For a starter, I tried forall { for (j = 0; j < nseg+1; j+=1 ) { diam(j/nseg) = diam(j/nseg)*1.0 } } but it changed the diameter a...

How can I customize the reaction rates? (Do you have a tutorial on it somewhere?) To be more concrete, I thought I could replace reaction = rxd.Reaction(2 * hydrogen + oxygen > water, 1.0) by reac_speed = 1.0*hydrogen**2*oxygen reaction = rxd.Reaction(2 * hydrogen + oxygen > water, reac_speed) It ru...

Thanks for the reply. The system was a mass-action reaction system, and the rates of all injected species were positive. But I finally managed to solve the problem by making the tolerance way smaller (down to 3e-9) than it used to be. The downside is of course that now my simulations are much slower...

Is there a way to force the concentrations to be non-negative? I'm using CVode and adaptive time step in a system of >100 reactions, and very often end up with negative concentrations for some of the species, although initial concentrations are all non-negative. Consequently (at least so it seems), ...

I have some questions to which I didn't find answers in the tutorial. 1) How can I record concentrations? Say, I would like to record the hydrogen concentration at location dend(0.5) into a vector in the example of https://neuron.yale.edu/neuron/static/docs/rxd/tut_main.html#simple-reaction-with-abr...