I have survived being The Lone Computationalist, and based on my experience, it is a terrible place to be. Long story short, you are at severe risk of achieving very little in your PhD unless your supervisor finds a collaborator with substantial MD experience who is willing to co-supervise you and co-author with your supervisor (and whom your supervisor is willing to co-author with).
This sort of situation would not be accepted in any other field of science. No supervisor (I hope!) would expect a PhD student with zero experience to run experiments with a microscope, fume hood, HPLC column, or laser table, without arranging prior training and follow-up mentoring from a lab tech or postdoc. And yet this is how students are often asked to approach MD. Maybe supervisors don’t feel they’ve lost anything because they don’t have to pay anything for LAMMPS or other packages. But they’ll have wasted a student and the student is left with much worse prospects after graduation. (There is even the physiological and psychological harm of sitting all day at a computer to account for – small, but not zero.)
To make this tangible: what will you do when you approach your supervisor, present your results, and find that you can’t line them up with experimental data? You will have to decide which of the following has happened:
- You did something wrong and need to start over.
- You did nothing wrong but you need to run longer to equilibrate your system and get good statistics.
- You did nothing wrong but it is not physically possible to run long enough to get good statistics.
- You did nothing wrong and your results are qualitatively correct – the real-life system is too complicated to get quantitative agreement.
- You did nothing wrong, the experimental papers are wrong.
I have personally experienced or seen all of the above. Deciding which of the above has happened, and either correcting it or arguing for it in a peer-reviewed journal article, is work worthy of a co-authorship and certainly requiring scrutiny during peer review. When a reviewer says you’ve used the wrong thermostat and the wrong short-range cutoff, you won’t be able to reply “But someone on the Internet said it was okay!” You need more guidance than that.
To be very clear, I have no doubt that you have the intelligence and perseverance that is needed to complete your PhD. But you do need the guidance of a dedicated supervisor or mentor, just the same as in any other field of research. And if your supervisor can’t find you that level of help (at least for your first paper) then your publication record, future career, and overall scientific effectiveness is being put in severe risk.
POST-EDIT: Here’s an easy and practical step to take: Reach out to the administrators of your local supercomputing cluster, and ask them which of their MD users might have the capacity to co-supervise your PhD or co-author your first paper. (You won’t be able to complete your PhD without relying on a cluster.)