Agents will have different sizes and compositions, and I think we could make their exact metabolic costs slightly randomized, though bigger agents would diffuse slower and be more likely to be specific or potent (maybe as an agent evolves, the formula to create it slowly changes too, getting bigger/smaller as the agent gets better, etc). For now, we could just throw any simple combination of a few amino acids and maybe a sugar or nucleotide or something.
Copied over from the parent thread:
That’s the logic that led me to produce the list I linked 
. In these equations I made sure to keep carbon balanced, ignored the production and incorporation of water since the amount of water turned over through chemical reactions is always very small compared to the amount of water a cell requires for all sorts of other reasons (ie, a scenario where water is a limiting factor in a reaction is a scenario where the cell has a whole lot of other problems), and used ATP not so much as a chemical compound, but as a unit of energy accounting, to quantify the number of ATP-equivalent units of energy usably produced, or required, by each reaction.
So, for example, you will note that the fat reactions don’t preserve pyruvate, but that’s ok since carbon is preserved, and excluding photosynthesis, ATP is generally lost in reaction cycles, as it should be, since the Gibbs potentials are what drive these reactions in a certain direction in the first place.
How are you driving reaction rates? I imagine you are doing a simple rate law thing. This is a problem with the current game too, since reaction rates in living cells are controlled heavily by gene expression, ligands, etc, and are thus not simply driven by the quantities of each reactant and product. The question is, how do we quantify those regulating factors?
I think what we need to do, just as much as producing a set of processes that doesn’t have any hidden perpetual energy sources, is come up with a specific rule for the rate of each process. For example, what determines the rate at which a cell produces ATP through respiration? Or glycolysis? Or deamination?