In 1870 John Tyndall said:
"An intellect the same in kind as our own would, if only sufficiently expanded, be able to follow the whole process from beginning to end. It would see every molecule placed in its position by the specific attractions and repulsions exerted between it and other molecules, the whole process and its consummation being an instance of the play of molecular force."
Computers are now powerful enough that they can track in detail the forces on a system and predict what will become of that system as a function of time. The methodologies are not perfect by any means. Just as in weather forecasting, chemical simulations cannot be run indefinitely, and there are limits on the accuracy that can be achieved. However, in general, computers can simulate many of the properties which might otherwise be measured in the laboratory. Tyndall's 1870 comment has been realized, not by an intellect, but by a set of machines programmed by scientists, based on the laws of nature.
The use of computers in understanding situations is now everywhere. Children, young and old, use computer games to understand sports and driving, tactics and strategy. The military rehearse their plans using war game simulations. Architects allow their customers to walk through virtual buildings. Economists plot out the behavior of the markets on the basis of financial models. All of these activities rely on microcomputers to calculate the possible interactions in the systems and present the important variables be they visual, audio, or numeric to the humans using the system.
Molecular simulations operate in the same way, just as Tyndall foresaw. The computer tracks the attractions and repulsions of the system in minute detail, if necessary tracking the behavior of electrons themselves. The computer then uses this information to put together processes from beginning to end.
Many examples from the worlds of chemistry and materials that have been explored using computers are collected in The Molecular Universe site.