Hi, please include the list email in your follow-ups so everybody can benefit!
To answer your questions: I wrote a little code that takes a single water molecule with the geometry described in the tip4p paper. The code the replicates the water molecule in to a cubic array, which is what you are seeing at the start of the simulation. I chose this structure because it is the easiest to replicate. It would be an extremely useful exercise for you to write your own code to do this, as once you figure out how to build one system, it’s just takes a little tweaking to build just about anything else you can imagine. Seems like one of the most common questions from new users on this list is “how do I get starting coordinates for X?”
Once you thermalize the system it will break up the symmetry. This is why it is important to let your simulations run a while before you try to collect any useful data. The size of the box is just based on a 1 g/cm^3 density for water at 25C. Another useful exercise would be to calculate this yourself.
Finally, I am modeling water based nanofluids with metallic particles so yes, I have water and metals together. In lammps you need to use a hybrid potential. I use tip4p for the water, eam for the metal and LJ for the water / metal interactions. You have to hunt for or generate the LJ parameters yourself. It’s not perfect and ignores some important chemistry but is a good first approximation. Attached is a paper I found which describes what I am doing. In theory COMB or REAXFF would do a better job in capturing the relevant chemistry / physics but they probably are not parameterized for your system of interest.
Good luck.
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