Hi,
This is a known shortcoming for nc trajectories with a small interval.
Most of these issues will be solved in the upcoming ATK-2017 version, where we use the HDF5 format to save MD trajectories. There will also be an option to disable storing velocities, forces, and stress to make the file size smaller.
For ATK-2016 the workaround to make it at least somewhat faster for such cases is that you switch off "Save trajectory" (or set in the script in the MolecularDynamics function), and instead make sure that you check "Save" in the Molecular Dynamics widget (or add a line nlsave('trajectory.nc', md_trajectory)
after the MolecularDynamics block in the script).
Then the trajectory is not saved on-the-fly during the simulation, but as a whole after the simulation has completed, which should be faster.