Flow ChartΒΆ

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 Getting started. Several steps of energy minimization may be necessary, these consist of cycles: gmx grompp -> gmx mdrun.

digraph flowchart {
node [ shape=box, width=1.5 ]

input_pdb [
  label="eiwit.pdb"
  tooltip="Protein Databank file"
  URL="file-formats.html#pdb"
  shape=none, width=0, height=0, margin=0
  group=input
]
pdb2gmx [
  label="Generate a GROMACS topology\ngmx pdb2gmx"
  tooltip="Convert PDB file to GROMACS coordinate file and topology"
  URL="../onlinehelp/gmx-pdb2gmx.html"
  width=3
  group=main
]

input_pdb -> pdb2gmx [ headport=e ]

editconf [
  label="Enlarge the box\ngmx editconf"
  tooltip="Adjust box size and placement of molecule"
  URL="../onlinehelp/gmx-editconf.html"
]

pdb2gmx -> editconf [
  label="conf.gro"
  labeltooltip="GROMACS coordinate file containing molecules from PDB file"
  URL="file-formats.html#gro"
]

solvate [
  label="Solvate protein\ngmx solvate"
  tooltip="Fill box with water (solvate molecule)"
  URL="../onlinehelp/gmx-solvate.html"
  width=3
  group=main
]

pdb2gmx -> solvate [
  label="topol.top"
  labeltooltip="GROMACS ascii topology file"
  URL="file-formats.html#top"
]
editconf -> solvate [
  label="conf.gro"
  labeltooltip="GROMACS coordinate file with adjusted box etc."
  URL="file-formats.html#gro"
]

input_mdp [
  label="grompp.mdp"
  tooltip="Parameter file from grompp (controls all MD parameters)"
  URL="file-formats.html#mdp"
  shape=none, width=0, height=0, margin=0
  group=input
]
grompp [
  label="Generate mdrun input file\ngmx grompp"
  tooltip="Process parameters, coordinates and topology and write binary topology"
  URL="../onlinehelp/gmx-grompp.html"
  width=3
  group=main
]

input_pdb -> input_mdp [ style=invis, minlen=3 ]

input_mdp -> grompp [ headport=e, weight=0 ]
solvate -> grompp [
  label="conf.gro"
  labeltooltip="GROMACS coordinate file with water molecules added"
  URL="file-formats.html#gro"
]
solvate -> grompp [
  label="topol.top"
  labeltooltip="GROMACS ascii topology file with water molecules added"
  URL="file-formats.html#top"
]

mdrun [
  label="Run the simulation (EM or MD)\ngmx mdrun"
  tooltip="The moment you have all been waiting for! START YOUR MD RUN"
  URL="../onlinehelp/gmx-mdrun.html"
  width=3
  group=main
]

grompp -> mdrun [
  label="topol.tpr"
  labeltooltip="Portable GROMACS binary run input file (contains all information to start MD run)"
  URL="file-formats.html#tpr"
]
mdrun -> mdrun [
  label="Continuation\nstate.cpt"
  labeltooltip="Checkpoint file"
  URL="file-formats.html#cpt"
]

analysis [
  label="Analysis\ngmx ...\ngmx view"
  tooltip="Your favourite GROMACS analysis tool"
  URL="../onlinehelp/bytopic.html"
]

mdrun -> analysis [
  label="traj.xtc / traj.trr"
  labeltooltip="Portable compressed trajectory / full precision portable trajectory"
  URL="file-formats.html#xtc"
]

energy [
  label="Analysis\ngmx energy"
  tooltip="Energy plots, averages and fluctuations"
  URL="../onlinehelp/gmx-energy.html"
]

mdrun -> energy [
  label="ener.edr"
  labeltooltip="Portable energy file"
  URL="file-formats.html#edr"
]
}

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Non-bonded cut-off schemes

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