High performance computing applications have increased tremendously the last decade or two, and it is now quite possible to simulate many processes that were completely impossible only a few years ago. Yet, many of the most important practical problems occur on scales of length and time that are several orders of magnitude beyond this, particularly in biochemistry/biology.
I will present some of the approaches we have used to overcome these limitations, and which have enabled us not only to simulate and model events that previously were considered "impossible", but also doing it with standard hardware instead of supercomputers.
This will be illustrated with examples from our recent work on folding of small globular proteins in water as well as understanding the entire process of how amino acids are inserted into bilayers to form membrane proteins, but many of the underlying modeling ideas are universally applicable.