| 
 | VERSION 3.3 | 
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 |  | tpbconv |   | traj.trr | |||||
|  |   | ||||||||
| Run the simulation (EM or MD) | mdrun |  |   | ||||||
|  |  | ||||||||
| traj.xtc | ener.edr | ||||||||
|  |  | ||||||||
| Analysis | g_... ngmx | g_energy |  | ||||||