MD Simulation with "colored" patchy particles

[BiagioValenti]

Hi!

I'm trying to implement a code to do a Molecular Dynamics simulation of patchy particles where the patches are "colored". This means that for every type of particle, each patch has an individual number (through the defining orientation vector) and can interact only with certain other patches with certain numbers following then an interaction matrix.
For example, If I have particle A with patches 1,2,3 and particle B with patches 4,5,6 I might for example say that the only allowed interactions are 1-1, 2-4, 3-5 and 6-6.
How can I implement this in HOOMD?

Thank you to everyone who can help me

[mphoward]

Provided there aren't THAT many different colors of patches, you can assign a different type to each color, then set the pair interaction parameters between colors according to your model. For example, you can set r_cut to zero to disable the interaction.

[BiagioValenti]

Thank you very much for your kind answer. However, I don't understand how I can implement this, given that class hoomd.md.pair.aniso.Patchy works with particle_type (as in [TypeParameter] [[tuple] [particle_type, particle_type], [dict]]). How can I give different colors to different patches on the same particle then?

[mphoward]

Sorry, your original post didn't include a description of how you wanted to implement your patchy particle model. I haven't used the potential that you referenced, but based on the documentation, I think you are right that it doesn't seem to assign a type to the patches. You might be able to still use it by making multiple instances with patches of different types assigned to each instance.

This may be somewhat inefficient, so an alternative approach would be to use a rigid-body model, for which it is definitely possible to assign different types to interaction sites that represent your patches. That is what I had in mind.

[joaander]

@mphoward is correct. In HOOMD-blue, all pairwise interactions look up parameters from a full N_types by N_types (symmetric) matrix. To tell HOOMD-blue that there is no 1-2 interaction, set the potential parameters to e.g. 0 and r_cut to 0. This was recently discussed in #2023 and has also been covered in tutorials such as https://hoomd-blue.readthedocs.io/en/v5.1.1/tutorial/08-Placing-Barriers-in-the-Simulation-Box/02-Fixed-particles.html.

This is true whether you are using MD simulations of rigid bodies or HPMC simulations with a union potential.

[BiagioValenti]

Thank you to both of you for your kind answers.
However, if I understand well, the interaction is always particle_type-particle_type and there is no way to define interaction between the singol patches on the same particle.
I solved using a rigid body, composed by physically identical particles, with each type representing a single color of the patches.