Boltzmann and elementary charge values

[bremen]

Hi.

I would need some help to translate an equation, I found on a paper, into the correct NEURON equivalent.

This equation controls the forward transition between two states in a markov chain.

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alpha = ao exp(eo zada E/kT)

ao is an integer calculate by the authors, eo is the elementary charge, zada is an integer calculate by the authors, E is the voltage, k is the Boltzmann constant, T is the absolute temperature.

I can "simply" replace the elementary charge and the Boltzmann constast with their actual values or is there a better way?

[ted]

Are you asking about a statement in a hoc or Python file, or in a mod file?

[bremen]

My bad, I forgot to write that the equation will be used in a MOD file.

[ted]

Regardless of the programming language, it is generally not a good idea to embed magic numbers (numerical constants) in code. Instead, it is best to use a variable whose value will not be changed during a simulation. In NMODL you could define a symbolic constant by declaring its name and assigning a numeric value to it, with appropriate units, in a CONSTANT block. However, the recommended practice is to do this in the UNITS block. For examples, see
https://nrn.readthedocs.io/en/8.2.6/pyt ... nmodl.html

[bremen]

Thank you.

I have added the two costant as UNITS and the MOD files pass nrnivmodl without issues.

[bremen]

Hi.

For nrnivmodl was ok but for modlunit is not and the voltage clamp showed that too.

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alpha = 50exp(e * 1.2 * v/(boltzmann *(273.15 + celsius)))
The previous expression needs the conversion factor (1000)

My issue is where i have to apply the conversion factor. If I simply multiply everything for 1000 it goes even worse.

[ted]

To give specific advice, I'll have to reproduce the error for myself. Can you email the mod file in question to ted dot carnevale at yale dot edu?