I have a system consisting of DNA and ions.
I want to put water molecules in my system.
These are my questions.
I want to use TIP3p model at the moment.
I know that I need to put the xyz coordinates of 2 hydrogens and 1 oxygen in lammps data file.
It has some angle between H-O-H and the bond between H-O.
So, initially, Do I need to calculate positions before I put 2H and O in the lammps data file ?
If I put 2H and O at random positions and I group atoms in input file, it is automatically moved
together with given bond length and angle under some potential ?
This is the first try, so I don't know how to start with water molecules in my system.
Please, help me.
Any suggestions is greatly appreciated.