Yes, there are a fair number of MD packages, each with their own benefits. For me, when choosing a package, I look for several things:
is the code currently maintained by some party, is there some sort of basic help available
Is the code written, distributed in such a manner that I can add functionality if need be
does the code have good parallel capabilities, is it portable to the machines I need to use
does it have the capacity to handle the geometry, loading I am interested in
does it have the potential(s) I need to use
The first one is actually usually the major deciding factor, as there are a number of packages mentioned in the literature that have more or less died or were never available to the public. The last 3 are also important - though the answer to these may vary depending on the problem being studied. I have used 2 packages in the last few years, Tahoe and LAMMPS - and while Tahoe has some nice features for implementing multiscale methods, it’s atomistics were a bit behind the continuum methods (particularly in parallelization, though that may have changed). LAMMPS on the other hand, I have found to be very capable for the problem I am currently working on since it relies entirely on large scale atomistic calculations.
Now, as to if MD (or empirical potential atomistics in general) will be the way to solve your problem - that will be something you will have to determine. It all depends on what you are interested in finding out.
Anyway, hope that helps,