commands

# remove crystalline water molecules
grep -v HOH 1ubq.pdb > 1ubq_clean.pdb

# load the required modules
module load gromacs/2018.8
module load gnuplot/5.2.8

# to run on gpu please load gromacs/2018.8-gpu module

# user response required to the following command, issue on head node
#Toplogy generation
gmx pdb2gmx -f 1ubq_clean.pdb -o 1ubq_processed.gro -water spce
#choose 15 0

#Make a box:
gmx editconf -f 1ubq_processed.gro -o 1ubq_newbox.gro -c -d 1.0 -bt cubic

#Solvation:
gmx solvate -cp 1ubq_newbox.gro -cs spc216.gro -o 1ubq_solv.gro -p topol

#Energy Minimization
# update em.slurm
gmx grompp -f em.mdp -c 1ubq_solv.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

# user response required to the following command, issue on head node
gmx energy -f em.edr -o potential.xvg
# choose 10 0

For Equilibration:
# update nvt.slurm and npt.slurm
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
gmx mdrun -deffnm nvt

gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
gmx mdrun -deffnm npt

check the graph
gmx energy -f npt.edr -o density.xvg
gmx energy -f npt.edr -o pressure.xvg


# user responce req

Run the simulation production:
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
gmx mdrun -deffnm md_0_1