Earlier quoted context omitted.
Again, i would assert that a cell is 70% water. some tiny fraction of water that's actually used in a reaction would just be special cased, and modeled independently. My understanding of "solution" is stuff floating in water. If there's some value in breaking out each atom, i'm all for it, but i kind of suspect the spherical cow is good enough in that case. Even if i'm wrong there, each atom would introduce at least…
The interior of a cell does not follow solution dynamics at all in the way that you would like for it to, and this is why: http://mgl.scripps.edu/people/goodsell/illustration/mycoplas...
I don't understand why it's easier to simulate each individual atom than it is to simulate things with structure. I would assume a simulation would regard the long yellow strands of dna as dna rather than the component parts.
I'm used to a world where having structure implies constraints. With constraints, simulation can avoid a bunch of special cases and is therefore faster. I find foobarbazqux's approach of simulating each atom upsetting. But that's ok. You guys seem to think it's the way to go, and you all get results. shrug
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I don't think simulating water is easy, but i believe it's likely easier to simulate water than it is to simulate all possible states of the constituant atoms.