Anyway....... the fastest 6-core CPU on the market is the i7-980x, and costs 1000$:D
The cheaper solution is the i7-970, which costs 900$ (rofl )
And the cheapest solution are the AMD X6 10xxT series, which cost 200$(1055T) and 300$(1090T). They're slower, not much though, but are ALOT cheaper.
Assuming that MD calculations are highly parallel, the 980X is potentially alot faster than the 1090T. If time is money, it may be worth the $1k investment. I don't do MD simulations though so I can't really say.