Yes. Do an internet search for "level set methods." There is a free toolbox for level set methods available on the MathWorks website. Under certain conditions, you may be able use a special case of level set methods called fast marching methods. These are much faster and simpler to implement. I suspect in your case you will need the full level set method.
Some years ago I played with level set methods and ended up implementing a fast marching method for my work. This is now a chapter in my dissertation. I don't go into much detail on level set methods, but I do describe the fast marching method in pretty good detail. There is a link to my dissertation at the bottom of this page:
Try to generate your initial polymer beads position using matlab (coarse grain), and use LAMMPS to apply temperature. Or you can use other MD software like Materials Studio to build the model and run your simulation. Good luck