## GROMACS
Flow chart

Main Table of Contents

VERSION 3.2
Sun 25 Jan 2004

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 |

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