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!
The first advice would be to use the correct forum category. “Materials Project” (the default) is not it.
That is too little information. What kind of interaction model do you want to use? What does “the shape” represent and what kind of force should it react to.
It is not so much a matter of molecules, but based on the fact that LAMMPS uses particles to represent materials. Those are often molecules, but this need not be the case. LAMMPS can also have coarse grained representations (DPD, CG-SPICA, CG-DNA), discrete element modeling (GRANULAR) or grid-free continuum models (PERI, SPH, MACHDYN, LATBOLTZ).
So you will have to either convert your shape into a collection of points and use one of the potentials, or implement some new representation for your “shape” that more correctly represents what you want to show.
Overall, from the little information that you provide it sounds more like you should be looking for some finite element modeling package rather than use LAMMPS.
As for features available in LAMMPS that seem related to your question: