I have heard and read this explanation and justification many times and it is not valid. I consider it not a smart idea (from both, you and your supervisor) to start research in a completely new area without having some in-person expertise at hand that can provide guidance and tutoring. That will run an extremely high risk of making trivial mistakes that would not happen to experienced researchers. Online forums and tutorials can help, but are no substitute. There is much more to running correct MD simulations than having something that will work run without errors. Thus if you don’t have the expertise at hand within your group, you (or rather your supervisor) need to reach out and find a sufficiently experienced collaborator (or more) and work with them and receive tutoring and advice from them. MD is much more a craft than a science and there are lots of things that are not written down, but still matter that you can really only learn from practicing along experienced people. Keep in mind that you are dealing with 50-60 years of combined experience of the entire research community that did/does MD. There is a lot of residual practical knowledge out there.