The problem with molecular modeling/ protein folding algorithms is that each molecule interacts with every other molecule. So, you have an n^2 problem. Sure, hueristics get this way down to nlogn but what fundamentally slows it is not the growth in computation but the growth in the data being pushed around. Each node needs the data from every node's last time step. For these problems, doubling the nodes of a cluster computer might not even noticeable improve the speed of the algorithm. When I was helping people run these, they were looking at a few milliseconds of computation for a small number of molecules that took a few weeks of supercomputer time. So lots and lots of computing generations were/are needed before we get anywhere close to what they want to model.