Im trying to understand what is the default phase in MD simulation, is it air or vacuum? What is the default pressure is it 1 atm? I know instantaneous pressure in simulations dont make sense, but there needs to be an average pressure of the system right? How do I find that? My pressure values seem very high to make any real meaning…and I am not applying any external pressure .
There is no “default” that is applicable to all simulations.
What is “normal” is something that you choose: with your geometry, with your boundary conditions, with for parameters, with your pair/bond/angle/etc styles and topology, with your choice of temperature and time integration, with your other choices that impact the forces in the system.
… then probably there is something wrong with how your have chosen to set up your system.