Since MD is the topic of your PhD, there surely must be someone in your department (ideally, one of your supervisor, advisor, or co-workers) which has this expertise. You definitely do not want to outsource this skill in a forum: no one has the time and dedication needed to provide university-grade higher education to online students.
Good luck for your research. If you have problems using LAMMPS:
- read the documentation for the specific command
- study the examples shipped with the source code
- search the forum, there is a lot of wisdom here
- last resort: post a new question when you are absolutely sure no one has asked that before.
And, of course, Please Read This First: Guidelines and Suggestions for posting LAMMPS questions