I am working on nucleic acid (NA). I have to add K(+) ions to study its behaviour. I want to keep the coordinates of NA molecule and K(+) fixed & allow water molecules to equilibrate. This step is necessary to prevent the fast diffusion of bare K(+) ions, unprotected by their solvation shells, towards NA. I want to carry out the following steps. 1) NA and K(+) fixed, water molecules are allowed to move (equilibrate) 2) NA fixed, K(+) and water equilibration 3) All three are free to move. I have generated the position restrain file (*.itp format) for K(+) by using .ndx file & genrestr command. My question is where and, how do I need to plug .itp file in topol.top.

Format of position restrain for K(+) is :

[ position_restraints ] ;

i funct fcx fcy fcz

141985 1 1000 1000 1000

141986 1 1000 1000 1000 : : here 141985 is the atom index of the first K(+) ion and so on.