With the slight danger that if the calculation terminate midway, nothing is saved at all... For safety, you might want to at least save with a large interval, say 1000 steps instead.
Alternatively, the xyz file format doesn't incur the same overhead, although it doesn't offer the same advanced analysis capabilities. But for a backup option it serves the purpose.
As for Linux vs. Windows, there is typically not a huge difference for this kind of simulations. More important will be to ensure all cores are utilized, because the classical potentials take good advantage of OpenMP threading. So if you don't see all 4 or 12 or however many core you have running atkpython, try setting MKL_NUM_THREADS=the number of cores (if you are using the Job Manager, make a parallel, multithreaded local machine and set the number of threads there).