Step Eight: Production MD
Upon completion of the two equilibration phases, the system is now well-equilibrated at the desired temperature and pressure. We are now ready to release the position restraints and run production MD for data collection. The process is just like we have seen before, as we will make use of the checkpoint file (which in this case now contains preserve pressure coupling information) to grompp. We will run a 10-ns MD simulation, the script for which can be found here.
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr gmx mdrun -deffnm md_0_10
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