Why aren't the Anton computers used more widely?
Protein dynamics occur in multiple different time scales. I myself is a person using MD simulation for my research. One reason I am not so much interested in ANTON is not it's cost, limited resource etc. It's rather because one extremely long simulation wouldn't help much at least for my research.
Protein's thermodynamics as well as kinetics all depend on free energy landscape which is a priori unknown. To directly compute free energy from simulation, you generally need multiple order of magnitude faster machine even than ANTON. However, there has been many techniques such as Umbrella Sampling that helps resolve this issue on computers in our lab.
I would appreciate it if I can run my Umbrella Sampling in ANTON but it would be so much waste of time to wait on the line if I can run the same simulation for a week in my workstation.
Another reason I can guess why ANTON has not been widely used is because of its specificity. ANTON does not run typical MD simulation packages such as GROMACS, NAMD, AMBER etc. All packages use same algorithm to run the simulation but the commands, file structures etc, are all different. Typical MD user would prefer to use package that he/she is familiar with. I am not sure how much I would have to study to get used to ANTON MD package but why bother if I am not desperate?
So in summary, only those users who are interested in actual trajectories of protein and water in millisecond time scale would want to use ANTON but not many others. Other than such purpose, there are many techniques and algorithms that would work better than running a single extremely long simulation.