| VERSION 3.1 |
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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(continuation) | |||||
Generate mdrun input file | grompp | ![]() |
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(after crash) | |||||||
topol.tpr | ![]() |
tpbconv | ![]() |
traj.trr | |||||
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Run the simulation (EM, MD or LD) | mdrun | ![]() |
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traj.xtc | ener.edr | ||||||||
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Analysis | g_... ngmx |
g_energy | ![]() |