GROMACS-A Molecular Dynamic Approach

NOTE : CREATE A BLANK FILE IN FOLDER AND NAME IT AS ions.mdp and copy the content over there and save it. Then perform the 5th command.

5.command : gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr

Files generated in folder : ions.mdp , ions.tpr , mdout.mdp

6.command : gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -neutral

Select option 13 (SOL)

Files generated in folder :1aki_solv_ions.gro #topol.top2#