Using simFunction Object in Simbiology when my stoichiometry depends on a model parameter

Hi,

Prevusly asked this question and my problem was solved. Now I have another question:

Link

I am working on a SimBiology code with Stochiometry depending on a parameter (DAR). The specise are calculated based on their concentrations (nmol/liter). The size of the component changes too which is based on repeated rules. I use SimFunction for paarmetrization, therefor as we discussed, I use rate rules for the specieses in which their concentration depends on DAR. The method was explained before in this thread. But I get the follwoing error. Is their any way to fix this error?

Rate rule for species 'PL_ext' is invalid. Species 'PL_ext' is in concentration and in a compartment with varying capacity. For this to be valid, the compartment capacity

must be varied by a rate rule.

Answer 1

[Arthur Goldsipe]

The error you report is intended to communicate that SimBiology does not allow the following the following combination of conditions:

• A species is in concentration.
• The concentration of that species is determined by a rate rule.
• The compartment (that the species is in) is determined by a repeated assignment rule or an algebraic rule.

One fix would be the one mentioned at the end of the error message: Replace the repeated assignment rule or algebraic rule with a rate rule that gives equivalent behavior.

Another option would be to change the species units to amount instead of concentration and use (species amount)/(compartment volume) anywhere you need to reference the concentration.