| VERSION 4.0 |
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 | ![]() |
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| Generate a GROMACS topology | pdb2gmx | ![]() |
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| conf.gro | topol.top | |||||||
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| Enlarge the box | editconf | ![]() |
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| conf.gro | ||||||||
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| Solvate protein | genbox | ![]() |
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| conf.gro | topol.top | |||||||
| grompp.mdp | ![]() |
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| Generate mdrun input file | grompp | ![]() |
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Continuation | ||||||
| topol.tpr | state.cpt | |||||||
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| Run the simulation (EM or MD) | mdrun | |||||||
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| traj.xtc / traj.trr | ener.edr | |||||||
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| Analysis | g_... ngmx |
g_energy | ![]() |
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