I am very new to MD. I have three lammps questions and one on MD in general:
1. In lammps, creating a region necessitates having a pre-defined lattice. But what if I am reading my data from a .pdb file and I have no lattice defined? It seems that some functionality is lost unless I am missing something.
2. How can I create some complicated geometry representing surface roughness? For instance, I have a surface of parallel layers of polymer chains (<<<I've gotten this far). Now I need to cut out some rows to create grooves (this looks straightforward). But then I need to cut in the perpendicular direction to create some pillar-like surface topology. The removed chains need to be replaced by hydrogen. Any suggestions that would make this easier? Would something like topotools help me in that problem?
3. Can lammps help when it comes to extracting PCFF parameters and potentials?
4. I am doing a basic water simulation where I start with a cube of H2O and let it morph into the natural equilibrium config., the shpere. The initial "shock" is causing the molecules to disperse too rapidly. Now I know this has to do with the initial spacing, but how do you go about this? I mean is there a specific method to calculate the best initial packing or do you learn this from experience? (I'd love to get a book on this: Chemistry books don't go beyond models. MD books don't say much besides how the simulation works "under the hood". I can't seem to find a reference with that kind of practical info)
I started doing this just this past month, so please go easy on me. Any help, whether answers or suggested readings/tools, is greatly appreciated.