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You are right about multi-compartment reactions, they are used for reactions between regions of a section or with the extracellular space. A possible solution to the problem of diffusion between a pre- and post-synaptic section is to use the node.include_flux. For example; Diffusion across a synapse...

Ted is right, CaDynamics_E2 writes to cai but it is then overwritten by rxd. Looking at the mod file it looks like it does a couple of things; calcium accumulation and restoration to minCa. RxD already handles accumulation, but unlike the mod file it uses the segment's area and volume to calculate t...

Sorry for the late reply. RxD will keep track of concentrations and update Nernst potentials of the `rxd.Species` in your model. It can also generate currents, but only when a charge carrier movers across a membrane, which can be defined with a `rxd.MultiCompartmentReaction`. Here is an example of t...

Sorry for the late reply. Current for MultiCompartmentReaction aren’t stored so cannot be directly recorded from. However by recording the contributing states, concentrations, etc. it is possible to calculate the current for any MultiCompartmentReaction. Here is an example comparing NEURON’s Hodgkin...

Sorry, Ted is right. It should be; for calcium concentration. I've edited my previous post.

I would define a species once for all the regions and then set the initial concentration using a function of the rxd.node. As you have several species, I would define a function for initialization, that checks the node attributes to determine which initial value to use. Also, I agree with Ted, 6e-3 ...

The f_rate and b_rate are the forwards and backward rates of the reaction, provided you are using mass_action=False, they are usually third and fourth positional arguments to rxd, (the backward rate is optional and None by default), for example; k_current = rxd.MultiCompartmentReaction(ki, ko, gk * ...

Hi, Sorry for the delay. The flux from rxd multi compartment reactions are not stored so can not be directly recorded. However it is possible to infer them by recording the relevant rxd states and species and substituting them into the the f_rate and b_rate. Here is an example rxd Hodgkin–Huxley mod...

Sorry, it looks like an issue with how `abs` is compiled in rxd reactions.
A simple workaround is to use the rxdmath fabs in your reaction scheme; Let me know if you have any further problems.

Hi, The problem is rxdmath.v is not a number, it is a symbol that is mapped to the membrane potential of a segment at runtime, so if-statements in the reaction scheme are not supported. However you can represent something like the if-statement using a thresholds; https://neuron.yale.edu/neuron/docs/...

Hi, If I have understood your question, you have something like; pump_current_na = rxd.MultiCompartmentReaction(nai, nao, 3.0*pump, mass_action=False, membrane=mem, membrane_flux=True) Where `nai` and `nai` are rxd Species on an intracellular and extracellular region and `pump` is the rate of the Na...

Thanks, you are right, the extracellular space was designed to be used at a macroscopic scale. The average volume that would be excluded in brain tissue is used to give the `volume_fraction` (typically 0.2) where substances are free to diffusion rather than excluding any particular voxel. However it...

Sorry for the late reply. 1. This is a great question, your workaround sounds reasonable. I don’t think it’s necessary to split the axon into multiple sections, just set nseg as required. An alternative solution is to use node.include_flux, here is a toy example using an nmodl mechanism to allow a l...

If `pmp_thr` is the only rxd mechanism producing a membrane flux for calcium then simply recording the calcium current (as you have `ca_cur`) is sufficient. Unfortunately if this is not the case the contribution of the current resulting from a particular MulticompartmentReaction is not directly acce...

Sorry for the delay, you're right about not using charge=0. Rxd reads the currents and then (if they have a charge or valence) divides it by the charge and scale it appropriately to determine the change in concentration. Unfortunately this does not work with charge=0. As you have found, to work arou...