GROMACS Flow chart Main Table of Contents

VERSION 4.0 Sun 18 Jan 2009

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			pdb2gmx
			conf.gro		topol.top
Enlarge the box			editconf
			conf.gro
Solvate protein			genbox
			conf.gro		topol.top
grompp.mdp
Generate mdrun input file			grompp
						Continuation
			topol.tpr			state.cpt
Run the simulation (EM or MD)			mdrun
			traj.xtc / traj.trr		ener.edr
Analysis			g_...     ngmx		g_energy