It most certainly exist outside secret labs :) Like Gerben wrote, the fields are called molecular dynamics (MD) and quantum chemistry which, as computers grow faster, will be essential tools of nanotechnology and medicine.
Molecular Dynamics is currently implemented by making certain approximations in that electron motion is not explicitely modelled. In practice, empirical forcefields are matched to experimental data and molecules are essentially modelled by summing the forces on each atom and using $F=ma$, then integrating the acceleration over time.
It's far from perfect - you usually can't match all measurable physical properties of a medium like water at the same time with the same forcefields. You can't normally model shifts of covalent bonds either since that involves changing the molecular composition which breaks the forcefield definitions. On the other hand, the methods are relatively quick and you can easily simulate systems of hundreds of thousands of atoms over a timescale of at least nanoseconds (microseconds if you have access to a supercomputer :). To interpret results you need some understanding of the deficiencies of the algorithms though.
Some interesting large simulations to date was of the protein factory, the ribosome, probably the evolutionary oldest complex part of life, and of a complete virus, the Satellite Tobacco Mosaic Virus. Below is a snapshot of a simulation I did of ion-channels in a cell membrane, you see a drug molecule bound in white in the center:
I would think that the most used (free) simulators are GROMACS and NAMD, with somewhat differing strengths but both are probably OK to start with. Usually paired with decent graphical tools to visualize what happens like PyMOL or VMD.
It's not particularly difficult to learn about this by writing your own simple simulator as well, if you're so inclined. In either case, simulating a 2x2x2 nm box of argon atoms or water-molecules for example illustrates many of the concepts.
Quantum Chemistry involves getting one step lower into the motion and shifts of the electrons. Thus you can simulate the breaking and bonding of covalent bonds and you don't have to rely on empirical forcefields for every molecule/atom you need in your simulation. However it's a lot slower computationally obviously (a factor of 100 at least? I'm not sure). You might use this to model in detail the mechanism of an active site in an enzyme for example.
The reason these are important fields for nanotech and medicine is that the simulations are the equivalents of the act of compiling and testing a program in computer software design, when it comes to designing new drugs and nano-scale machinery or materials. Essentially you want methods to test your ideas without manufacturing them first, and computer simulations take advantage of Moore's law which says that computing power doubles every 18 months...