In order to perform useful computer simulations on protein molecules, models that combine atomistic and continuum approaches will be necessary. The use of continuum models will reduce the number of system variables and allow studies of longer time scales. On the other hand, one will still need to retain atomic detail in certain parts of the protein molecule, such as an enzyme active site. Most of the important advances to date have been continuum models of the surrounding solvent, but simplified descriptions of the protein itself also are being developed. Finally, in order to study these several different levels of complexity simultaneously in a single simulation, it will be necessary to use modern software engineering techniques.
Huber, G. A. (1998, March). Future directions for combining molecular and continuum models in protein simulations. Progress in Biophysics and Molecular Biology. https://doi.org/10.1007/s10584-009-9706-z