I have a new structure that I want to analyze (lets just call it a shape). For the shape, I have the coordinates that make it up. I even have a tcl script in VMD that allows me to create the shape using graphics (draw triangle and draw lines). However, I want to simulate the shape in response to force. I know the best way to do this is to use LAMMPS.
How do I do this? All the tutorials I find online use molecules, which makes sense since it is molecular dynamics, but I want to specifically analyze a shape.
Is there a way I an input constraints from VMD into LAMMPS and test that, or something like that?
Thank you for the help, I am new to this so any guidance would be greatly appreciated!