Flow Chart
	Main Table of Contents	VERSION 5.0

This is a flow chart of a typical GROMACS MD run of a protein in a box of water. A more detailed example is available in the Getting Started section. Several steps of energy minimization may be necessary, these consist of cycles: grompp -> mdrun.

eiwit.pdb
Generate a GROMACS topology			gmx pdb2gmx
			conf.gro		topol.top
Enlarge the box			gmx editconf
			conf.gro
Solvate protein			gmx solvate
			conf.gro		topol.top
grompp.mdp
Generate mdrun input file			gmx grompp
						Continuation
			topol.tpr			state.cpt
Run the simulation (EM or MD)			gmx mdrun
			traj.xtc / traj.trr		ener.edr
Analysis			g_...     gmx view		gmx energy