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@shirshak55
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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