Several steps of energy minimization may be necessary,
these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
-.. URL="file-formats.html#pdb"
-.. ../programs/gmx-pdb2gmx.html
-
.. digraph:: flowchart
node [ shape=box, width=1.5 ]
pdb2gmx [
label="Generate a GROMACS topology\ngmx pdb2gmx"
tooltip="Convert PDB file to GROMACS coordinate file and topology"
- URL="../programs/gmx-pdb2gmx.html"
+ URL="../onlinehelp/gmx-pdb2gmx.html"
width=3
group=main
]
editconf [
label="Enlarge the box\ngmx editconf"
tooltip="Adjust box size and placement of molecule"
- URL="../programs/gmx-editconf.html"
+ URL="../onlinehelp/gmx-editconf.html"
]
pdb2gmx -> editconf [
solvate [
label="Solvate protein\ngmx solvate"
tooltip="Fill box with water (solvate molecule)"
- URL="../programs/gmx-solvate.html"
+ URL="../onlinehelp/gmx-solvate.html"
width=3
group=main
]
grompp [
label="Generate mdrun input file\ngmx grompp"
tooltip="Process parameters, coordinates and topology and write binary topology"
- URL="../programs/gmx-grompp.html"
+ URL="../onlinehelp/gmx-grompp.html"
width=3
group=main
]
mdrun [
label="Run the simulation (EM or MD)\ngmx mdrun"
tooltip="The moment you have all been waiting for! START YOUR MD RUN"
- URL="../programs/gmx-mdrun.html"
+ URL="../onlinehelp/gmx-mdrun.html"
width=3
group=main
]
analysis [
label="Analysis\ngmx ...\ngmx view"
tooltip="Your favourite GROMACS analysis tool"
- URL="../programs/bytopic.html"
+ URL="../onlinehelp/bytopic.html"
]
mdrun -> analysis [
energy [
label="Analysis\ngmx energy"
tooltip="Energy plots, averages and fluctuations"
- URL="../programs/gmx-energy.html"
+ URL="../onlinehelp/gmx-energy.html"
]
mdrun -> energy [