Flow ChartΒΆ
This is a flow chart of a typical GROMACS MD run of a protein in a box of water. 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="../reference-manual/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="../reference-manual/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="../reference-manual/file-formats.html#top"
]
editconf -> solvate [
label="conf.gro"
labeltooltip="GROMACS coordinate file with adjusted box etc."
URL="../reference-manual/file-formats.html#gro"
]
input_mdp [
label="grompp.mdp"
tooltip="Parameter file from grompp (controls all MD parameters)"
URL="../reference-manual/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="../reference-manual/file-formats.html#gro"
]
solvate -> grompp [
label="topol.top"
labeltooltip="GROMACS ascii topology file with water molecules added"
URL="../reference-manual/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="../reference-manual/file-formats.html#tpr"
]
mdrun -> mdrun [
label="Continuation\nstate.cpt"
labeltooltip="Checkpoint file"
URL="../reference-manual/file-formats.html#cpt"
]
analysis [
label="Analysis\ngmx ..."
tooltip="Your favourite GROMACS analysis tool"
URL="cmdline.html#commands-by-topic"
]
mdrun -> analysis [
label="traj.xtc / traj.trr"
labeltooltip="Portable compressed trajectory / full precision portable trajectory"
URL="../reference-manual/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="../reference-manual/file-formats.html#edr"
]
}](../_images/graphviz-546f8676b043be7a824d2ab2320a5e60473f82fc.png)
This is a flow chart of a typical GROMACS MD run of a protein in a box of water. Several steps of energy minimization may be necessary, these consist of cycles: gmx grompp -> gmx mdrun.