wrote and executed this script:

#!/bin/bash

###############################################################################
##                                                                           ##
## Hello!                                                                    ##
## Please contact me if you have any questions                               ##
## Contact Info:                                                             ##
## email: edward.kj1299@hotmail.com                                          ##
##                                                                           ##
## Code Inspiration from Bevan Lab's Gromacs Tutorial                        ##
##                                                                           ##
###############################################################################


###################################
#####         pdb2gmx         #####
###################################
gmx pdb2gmx -f 13merDNA_Mutant.pdb -ignh -o complex.gro
#choose amber99SB
#choose tip3p for water

###################################
#####   Make clamp POSRES     #####
###################################
gmx genrestr -f ssBNA9_fixed4_GMX.gro -o posre_ssBNA9_fixed4_GMX.itp -fc 1000 1000 1000

choose: 2 (BNA)

###################################
#####        Combine          #####
###################################
#combine the .gro files
    #make sure to change the number of atoms in the system
    #copy and paste the clamp atoms into the file

#edit the topol.top file
    #add the following near the top:
    
    ; Include ligand topology
    #include "ssBNA9_fixed4_GMX.itp"
    
    ; Ligand position restraints
    #ifdef POSRES
    #include "posre_ssBNA9_fixed4_GMX.itp"
    #endif

    #and the following to the bottom
    #like this:
   
    [ molecules ]
    ; Compound        #mols
    Protein_chain_A     1
    BNA                 1
    
    
# then position restrain the DNA
#Add the following to posre.itp (including the hashtags)

#ifdef POSRES_B
#include "posre_DNA_chain_B.itp"
#endif

###################################
#####         solvate         #####
###################################
gmx editconf -f complex.gro -o newbox.gro -center 4.5 4.5 9 -box 9 9 11 -rotate 90 190 0
gmx solvate -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top

    #look at the pbc in vmd with this command > pbc box


###################################
#####        add ions         #####
###################################
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1
#select SOL
# NaCl was used in the Tm value experimentation

gmx grompp -f minim.mdp -c solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -v -tunepme -deffnm em


    #for optimization with mpi (Does not work for my system)
    gmx tune_pme -s em.tpr -g -mdrun 'gmx_mpi mdrun' -np 12

    #for viewing purposes
    gmx trjconv -s em.tpr -f em.trr -o em_noPBC.xtc -pbc mol -ur compact

###################################
#####       Make INDEX        #####
###################################
gmx make_ndx -f em.gro
> 1 | 2
> q

###################################
#####           NPT           #####
###################################
gmx grompp -f npt.mdp -n index.ndx -c em.gro -p topol.top -o npt.tpr
gmx mdrun -v -tunepme -deffnm npt

    #took about 10 minutes    
    
    #for viewing purposes
    gmx trjconv -s npt.tpr -f npt.trr -o npt_noPBC.xtc -pbc mol -ur compact

###################################
#####        Pulling          #####
###################################
gmx grompp -f md_pull.mdp -c npt.gro -n index.ndx -p topol.top -t npt.cpt -o pull.tpr
gmx mdrun -v -tunepme -s pull.tpr
#pull takes approx. 60 minutes
gmx trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep #choose system

    #for viewing purposes
    gmx trjconv -s pull.tpr -f traj_comp.xtc -o pull_noPBC.xtc -pbc mol -ur compact

    #to generate a pdb from a gro file without waters in vmd
    set selection [atomselect top "not water"]
    $selection writepdb npt_no_waters.pdb



#to see box coordinates in vmd
molinfo 0 get {a b c alpha beta gamma}

###################################
##### After Pull INDEX        #####
###################################
gmx make_ndx -f npt.gro -o index2.ndx
> del 6
> del 2
> q

#edit the perl script:
    #change the for loops to match the amount of conf$i.gro files produced
    #change the index.ndx input to the name of the index file used
    
#read the summaries after running the perl script
#then choose certain files with coordinates in summary_distances.dat
    #took about 22 hours up to this point


#to correctly read the histogram
xmgrace -nxy histo.xvg