GROMACS Flow chart Main Table of Contents

VERSION 3.1 Wed 27 Feb 2002

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						(continuation)
Generate mdrun input file			grompp
						(after crash)
			topol.tpr				tpbconv		traj.trr
Run the simulation (EM, MD or LD)			mdrun
			traj.xtc		ener.edr
Analysis			g_...     ngmx		g_energy