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Ok. So, there is no change in cai in the model and it may not be the reason for the message. I will try find the source of error. Meanwhile, I will use a workaround for calculating transfer impedance similar to as discussed in the above posts: injecting current (1 nA) and recording the resulting (pe...

Sorry for not being clear on the source of mod files. I obtained the cachan.mod and capmp.mod from C:\nrn\examples\nrniv\nmodl of my NEURON 7.6.2 setup. Also uploaded here: https://drive.google.com/drive/folders/1ZGvLL3qKvjmCe7klT9rwk6L93qY-xQuh?usp=sharing The SUFFIX in capmp.mod is capr. I don't h...

Thanks Ted for the detailed explanation for the "Warning". I will look into my model for the source of that error. Below is the code I used for the toy model: load_file("nrngui.hoc") v_init=-65 create soma soma{ nseg =9 insert hh insert cachan insert capr } finitialize(v_init) ob...

Hi Ted, I have a model with calcium accumulation mechanism. I wanted to measure transfer impedance at different locations of the cell using the Impedance class. While doing so I get a following error: cmplx_spFactor error: Singular The model does not have the extracellular and LinearMechanism. Accor...

Hi Ted, I was able to compile the alpha version of the code successfully but with some warnings. I used python3 for the process. Some of the warnings were related to deprecated NumPy API: /home/mpiuser/.local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning...

Hi, 1. I am trying to compile NEURON 7.6.2 source code on Ubuntu 18.04.1. I have got these files from https://neuron.yale.edu/ftp/neuron/versions/alpha/ : [ ] iv-19.tar.gz 2018-08-01 16:42 1.2M [ ] nrn-7.6.2.tar.gz 2018-08-15 13:27 7.8M (The source code at https://www.neuron.yale.edu/neuron/download...

Hi, I am trying to achieve resting ionic concentration balance in the extracellular and the intracellular environment where 2 cells are closely apposed to each other. The changes in concentration also results in unstable RMP of the cells. The pas mechanism current which was inserted to make the rest...

Thanks Adam! I will test this out and if I have any doubts I will get back to you.

Regards,
Darshan

Thank you, Ted.

I will try the model with RxD.

Hi, I have 2 cells that share the same ECF. The currents through both the cells can change the ECF concentration of all the ions. I have enabled this sharing using pointers e.g. for ion X, the extracellular concentration [X]o can be changed by cell1 (del[X]o,1) and by cell2 (del[X]o,2) (The change i...

Thank you, Ted for the quick reply! Sorry for the typo. Yes, it is 17%. Yes, caer is a state variable and not a constant. I have initialized it with a resting value in the INITIAL block. I will analyze the results by changing parameters and check to see if I get the desired output. I will also look ...

Hi, I have a 1-D shell calcium dynamics model with intracellular release and uptake mechanisms. I wanted to implement the volume distribution for cytoplasm and ER similar to what has been done in rxd.This can give me changes in the cytoplasm and ER calcium for different simulations. My model assumes...

Thank You, Ted! I was able to use the code bits you suggested in the gap junction model. For the exercise you suggested, if we have 2 parameters s1 (for permselectivity of K+) and s2 (for permselectivity of Na+) such that, s1=0.9, s2=0.1 (thus, s1+s2 =1), with following lines in the BREAKPOINT block...

Hi, Is it possible to implement Nernst-Planck Electrodiffusion equation (https://en.wikipedia.org/wiki/Nernst%E2%80%93Planck_equation) using NEURON-Python or Rxd for communication between 2 cells via a gap junction? I was looking ways to make gap junction current change both the membrane potential (...

Thank you, Michael!

I did the changes in units and compared the results using the original and the transformed files (without LONGITUDINAL_DIFFUSION). The results were similar. The longitudinal diffusion also worked well when added to the model.

Regards,
Darshan