Before revision:  Applying these strategies, we obtained near ideal strong scaling on up to 384 cores (16 nodes) . We summarize our lessons-learned in guidelines and strategies on how to take advantage of the available HPC resources to gain good scalability and potentially reduce trajectory analysis times by two orders of magnitude compared to the prevalent serial approach.
After revision:  Applying these strategies, we obtained near ideal strong scaling on up to 384 cores (16 nodes) , thus reducing trajectory analysis times by two orders of magnitude compared to the prevalent serial approach.