//used biotin generated by spartan but changed all atom names to be unique

acpype -i biotin.pdb

//copied .gro and .itp
//created system.top

gmx solvate -cp biotin_GMX.gro -cs spc216.gro -box 5 5 5 -p system.top -o system.gro

grompp -f em.mdp -c system.gro -p system.top -o em.tpr
mdrun -v -deffnm em
trjconv -s em.tpr -f em.trr -o em.xtc -pbc nojump
vmd system.gro em.xtc

grompp -f md.mdp -c em.gro -p system.top -o md.tpr
mdrun -v -deffnm md
trjconv -s md.tpr -f md.trr -o md.xtc -pbc nojump
vmd em.gro md.xtc