Molecular Dynamics Simulation Steps Gromacs software

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
 

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