Christina, it's amazing how those guys are pussy-footing around when each and every one of your examples is grammatically correct and in ordinary English all of them have exactly the same meaning …
Simulations of protein volumes
Simulations of volumes of proteins
All your examples make it abundantly clear that while you might in fact mean only one, you are potentially talking about more than one simulation or more than one protein or more than one volume, any of which will necessarily force the whole sentence and anything associated with it into plural form.
Even though the result might be the same, I'm sorry to say that Au101's heads and hands might be misleading…
'Drawings of heads of famous people' doesn't imply that famous people each have more than one head, but neither does it imply that there's more than one head depicted in "the drawings".
It does imply that in each and every drawing under consideration, there is at least one head of a famous person. Is it clear that "more than one head in the drawings" is very different from "at least one head in each drawing"? That the second means exactly what it says on the back-stamp but the first could as easily describe two or three heads in 27 drawings?
In the same way, when one says 'raise your hands' to a group of people, they are expected to raise only one hand each and the plural "hands" is needed to match the plural "people".
Given that "simulations" is rather abstract, it could as easily take the singular "simulation" but that and almost anything else other than that each of your examples is just fine, is a matter of personal taste, in ordinary and in your kind of technical English.