Is there any command in lammps by which i can add water molecules to the graphene surface ?
The easiest way to do this is to create a file containing the atomic coordinates and the bond topology (bonds, angles, dihedrals, impropers). In LAMMPS all of this information is contained in a single file called a “data” file. The format of a LAMMPS data file is explained here:
If you don’t want to create your own data file, there are several “molecule builder” tools available which might be useful:
I think that topotools/VMD, moltemplate, and EMC can create a data file that you described.
(With EMC, I’m not sure if you can control the orientation of the graphene sheet. Perhaps you can. But you can definitely create graphene sheets which lie in the XY plane using topotools. You can also build this kind of system with moltemplate. Example here. But moltemplate does not add bonds between nearby atoms. In that example, the carbon atoms are rigid. Yhere are some tricks you have to use if you want to add explicit bonds between the carbon atoms in the graphene using moltemplate. I can elaborate on this topic later, if you like.)
it is also possible to use a molecule file for water and the create_atoms command in LAMMPS with the suitable settings.
when loading a data file or creating a simulation box, suitable space for atom types and per-atom data needs to be reserved with the corresponding “extra” keywords.