For those just starting out with GROMACS and / or Molecular Dynamics Simulations it can be very daunting. It is highly recommended that the various and extensive documentation that has been made available for GROMACS is read first, plus papers published in the area of interest.
GROMACS Reference Manual - very detailed document that can also act as a very good introduction for MD in general.
Flow Chart- simple flow chart of a typical GROMACS MD run of a protein in a box of water.
Molecular dynamics simulations and GROMACS introduction (slides, video) - force fields, integrators, control of temperature and pressure (Berk Hess).