acpype -i cyclohexane.pdb

//copied .top, .itp, and .gro to folder

genbox -ci cyclohexane.gro -nmol 500 -box 5 5 5 -o cyclohexane_box.gro

genbox -cp cyclohexane_box.gro -cs spc216.gro -p cyclohexane.top -o biphase.gro


/////////////////Done up to here

grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr
mdrun -v -deffnm em -nt 6