Created
July 1, 2020 08:55
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# 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 |
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