help

Hi Dear LAMMPS users

I want to simulate an aqueous solvent (H2O , NaCl ), but I don’t know how can i build molecules of this structure in LAMMPS? Please help me.

Thanks a lot for your advice

M.Rezaei

This is not a very complicated system to build on your own, and it’s probably good practice as a beginner in molecular simulations to build something like this. You can proceed in one of a number of ways:

(1) Write a script that builds the entire system. The documentation for the read_data command outlines the required elements of the input file in extensive detail.
(2) Use a workflow in which you create PDB files for the sodium ion, the chloride ion, and a sample water molecule, and use a program like Packmol to create the required number of copies, then import to VMD to produce a LAMMPS data file.
(3) Something in between these two extremes (for instance, specify positions of Na+ and Cl- ions, then use “solvate” tool in VMD to add waters.

—AEI

As above mentioned, You can use Packmol that is simple and available at http://www.ime.unicamp.br/~martinez/packmol

Farrokh