gro file

itp file
force field?
what basis u select force field?
look into how many types of boxes are there?
why do u vaccum minimization?
what does the bond order mean for a protein
why do we do this solvent minimization
what is the difference between vacuum and solvent minimaztion
what does the ensemble means? what are the different kinds of ensemble
why in order of nvt and npt
read about rmsd, rmsf and radius of gyration (formulae and all)