Patchy Particles via Rigid Body Dynamics

[anisha-yeddanapudi]

Hi,
I'm new to hoomd-blue and have been attempting to simulate patchy particles using hoomd's rigid body MD. However, my constituent particles separate from the central particle whenever I run the simulation. How do I prevent this from happening?

Thanks!

[joaander]

Try reading the tutorial: https://hoomd-blue.readthedocs.io/en/v4.9.1/tutorial/06-Modelling-Rigid-Bodies/00-index.html

[joaander]

Can you show where specifically they are "splitting apart"? In your image, I see two blue spheres at the expected positions relative to each red sphere after mentally accounting for the periodic boundary conditions.

[anisha-yeddanapudi]

My concern was that there are some blue spheres that are unattached to the red central particles. If this is a result of the periodic boundary conditions, is there a way to deactivate this condition such that the box has rigid walls.

[joaander]

No, but you can place barriers: https://hoomd-blue.readthedocs.io/en/v4.9.1/tutorial/08-Placing-Barriers-in-the-Simulation-Box/00-index.html

[mphoward]

Or save the image flags in your GSD file, and unwrap the particles for visualization purposes!

https://hoomd-blue.readthedocs.io/en/v4.9.1/module-hoomd-write.html#hoomd.write.GSD

[anisha-yeddanapudi]

Thank you so much for the responses! After considering the barriers and periodic boundary conditions, the simulation works as desired. Much appreciated!