A huge source of uncertainty in molecular dynamics comes from the force model, which are crude approximations of electronic structure.  There is a great deal of active research on improved force models, many of which are implemented in AMBER (<a href="http:&#x2F;&#x2F;ambermd.org" rel="nofollow">http:&#x2F;&#x2F;ambermd.org</a>) and can be used from most popular MD packages.  Other approximations, such as the cut-off for short- vs long-range force evaluation, must also be validated.<p>Anton is built for a very specific configuration; the modeling assumptions may or may not be valid for a given scientific or engineering experiment.  Its value is in being able to rapidly experiments for which the modeling assumptions have already been validated (and run those configurations for longer simulated time), but not for questioning the modeling assumptions or for developing better models.