Flow Chart ========== 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 :doc:`getting-started`. Several steps of energy minimization may be necessary, these consist of cycles: :ref:`gmx grompp` -> :ref:`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" ]