I'm writing a simple molecular dynamics simulation software and I'd like to visualize its results with pymol. More in detail I have to simulate the behavior of chain of bounded monomers (a polymer) in certain conditions. The monomers are _generic_, i.e. I don't want to specify any particular element for them (one good thing could be specifying their diameter). I'd like to show the bonds between the monomers.
Which file format should I use for my output? At the moment I'm trying with XYZ, but its quite unsuitable for the things I've just remarked. Sorry for the eventual trivial question, but I'm a newbie in MD. Thank you, p.
