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The terminal command to be used in order to produce the
binary input file in accordance with the minimization protocol is
the following:
gmx_d grompp -f nvt.mdp -c em.gro –n index.
ndx –r em.gro -p topol.top -o nvt.tpr
Fig. 7 A model protocol file for the equilibration process in the canonical ensemble (NVT)
Sofia Kiriakidi and Thomas Mavromoustakos