[marcosdumay]

Hyperthreading is basically a way to emulate multiple cores, but sharing the more rarely used units (like floating point) between them. This way, a normal application can use the multiple cores, and actually run in parallel most of the time. You save a lot of silicon area, but when both threads try to execute the same rare instruction at the same time, they can't run in parallel.

The problem of molecular simulation is that it's almost entirely composed of floating point instructions. Thus, hyperthreading can't run them in parallel at all.