acpype -i cyclohexane.pdb

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

genbox -ci cyclohexane_GMX.gro -nmol 500 -box 4 4 4 -o cyclohexane_box.gro

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

//added 255 mols of cyclohexane to .top

//added #include "amber99sb.ff/forcefield.itp" and #include "amber99sb.ff/spc.itp" to .top

//commented out defaults directive in .top (because it was conflicting with the amberff I added.

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

vmd em.gro em.trr


/////////////////done up to here

grompp -f pr.mdp -c em.gro -p cyclohexane_GMX.top -o pr.tpr
nohup mdrun -deffnm pr -nt 6

grompp -f md.mdp -c pr.gro -p cyclohexane_GMX.top -o md.tpr
nohup mdrun -deffnm md -nt 6