I am trying to simulate rigid self-propelled rods. Currently, I am using a bead chain model with the fixes brownian for brownian motion, propel/self for propulsion, and harmonic bonds and angle potentials. These do keep my rods rigid to some extent but it is not perfect. I tried to use fix rigid to make them perfectly rigid but it doesn’t work well with fix brownian and is giving me very weird dynamics. (As forewarned in the LAMMPS documentation too)
I was wondering why this happens and how I could get around this problem and I would appreciate any input from experts.
You will not likely find any experts in this subject matter here. The combination of properties for your particles is quite uncommon. I can’t help you either, but when you cannot find a fix or combination of fixes that do what you need them to do, you usually will have to do some C++ programming and program a fix that does what you need, i.e. a variant of fix rigid that knows how to do brownian dynamics and can handle self-propelled objects. This is how many features in LAMMPS came into existence and this is why we put a lot of effort into making it easy to extend and modify LAMMPS.