Molecular Dynamics Simulation using Gromacs software
Here, For the protein pdb 1AKI, MD simulation has to be run for 1 nanosecond in water as a solvent
Install Gromacs in Ubuntu Linux: type the command: "sudo apt-get install gromacs" in command terminal
keep your PDB file in a new folder create in Desktop. Now in command terminal type: "ls"
check that your location is correct or not. If not, go to your folder location containing pdb file by typing "cd .."
Then type the following commands
Install Gromacs in Ubuntu Linux: type the command: "sudo apt-get install gromacs" in command terminal
keep your PDB file in a new folder create in Desktop. Now in command terminal type: "ls"
check that your location is correct or not. If not, go to your folder location containing pdb file by typing "cd .."
Then type the following commands
Step 1: pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce -ignh
opls force field (5)
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.8 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA+ -nname CL- -nn 8
grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
mdrun -deffnm nvt
grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -o npt.tpr
mdrun -deffnm npt
grompp -f md.mdp -c npt.gro -t npt.trr -e npt.edr -p topol.top -o md_0_1.tpr
mdrun -deffnm md_0_1
