www.neuron.yale.edu

I implemented the calcium buffer and diffusion model as described in the NMODL article. After I specified in my hoc file: cai = 1e-4, the cai used in the model was actually 5e-5. I added "VALENCE 2" to the "USEION ca" line, but that didn't solve the problem. Any help will be highly appreciated. Thanks.

Zhuo

no matter what value I give in the hoc file.
[code]
forall {
insert cadif
cao = 2
cai = 1e-4
}
[/code]

By "NMODL article" I presume you mean the expanded version of the
article
Hines, M.L. and Carnevale, N.T. Expanding NEURON's repertoire of
mechanisms with NMODL. Neural Computation 12:995-1007, 2000.

There are several different ways to initialize ionic concentrations,
and the "correct" one depends on the implementational details of
the mechanisms that affect the ionic concentration in question.
The best guide to initializing ionic concentrations is chapter 8
of the NEURON Book. You can pick up a preprint of this from
http://www.neuron.yale.edu/ftp/ted/book/revisions/
You will also find a more up-to-date version of our old NMODL
article in chapter 9.