Flow Chart

Main Table of Contents VERSION 5.0

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  
Generate a GROMACS topology  gmx pdb2gmx 
conf.gro topol.top




Enlarge the box   gmx editconf  
conf.gro
Solvate protein  gmx solvate 
conf.gro topol.top
grompp.mdp  
Generate mdrun input file   gmx grompp  
Continuation
topol.tpr   state.cpt  

Run the simulation (EM or MD)  gmx mdrun 
traj.xtc / traj.trr ener.edr
Analysis   g_...  
  gmx view  
  gmx energy  


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