I am a 6th year PhD in computational chemical engineering. I have extensively used Lammps for my Molecular dynamics simulations. However there are many aspects of the modeling tools that I have no idea about ( like the time integration procedures used, the algorithms to make parallel computing possible...etc). This makes me feel bad about myself. I know that it is not possible to know everything and an important part of PhD is research output, so not all attention can be diverted into learning everything about the tool.
But, my question is, what to do if that bothers me greatly? I don't feel like a potential expert in my research and I feel like that's something to worry about.
How does one feel like an expert or become confident about their research/technical abilities? Does that come from acknowledgement of the deficiencies and being humble of the fact that probably I won't know many aspects of many things?
Are there any advice you would like to give a new PhD graduate to ensure a satisfying research career?