Need Guidance: Implementing Depletion Interaction for Beginners in HPMC Tutorial

[Nikhil Menda]

Hello HOOMD-blue Community,

I'm an absolute beginner with HOOMD-blue, currently working through the HPMC tutorial. I've become intrigued by the challenge of implementing depletion interactions, particularly for simulating lock and key colloids.

My understanding of colloidal physics is still in its early stages, and I'm eager to integrate depletion interactions into my simulations. However, I'm not quite sure how to do so.

Here are my specific questions and concerns:

Beginner-Friendly Advice: What's the most accessible approach for a beginner to implement depletion interactions in the HPMC tutorial context? Are there any tutorials out there specific to the depletion interaction?

Parameter Selection and Setup: Guidance on setting up system parameters for such simulations would be very helpful. I'm particularly looking to understand the relationship between the size and concentration of depletants and the colloidal particles.

Validating the Simulation: How can I ensure that the depletion interaction is functioning correctly? Are there specific indicators or data points I should be monitoring?

Resources for Beginners: I would appreciate any beginner-friendly resources, tips, or examples.

To give you a better idea of where I'm at, here's what I've tried so far in initializing the simulation:

I'm excited to learn more and appreciate any assistance you can provide. Thank you!

Regards,
Nikhil

[Joshua Anderson]

Nikhil,

I am not aware of any beginner-friendly resources for implicit depletants. The only information on the method is in the author's publication on the algorithm (https://dx.doi.org/10.1063/1.4935175). The code has been rewritten with new algorithms several times since that publication. The only documentation on those rewrites are the commit comments and pull request descriptions.

The author of the implicit depletants algorithm has moved to a new position and no longer maintains the code. There are also open bugs in the code which no current developer knows how to fix: https://github.com/glotzerlab/hoomd-blue/issues/1448. I plan to deprecate implicit depletants and remove the feature in HOOMD-blue 5: https://github.com/glotzerlab/hoomd-blue/issues/1651. I would suggest that any researchers working in this area develop, test, and validate their own implicit depletant code. The code from HOOMD-blue will be availalbe in the git history for anyone to access. I would suggest either developing your own custom code or implementing the method as in HOOMD-blue via an external component.

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Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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I'm excited to learn more and appreciate any assistance you can provide. Thank you!

Regards,
Nikhil

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[Nikhil Menda]

Thank you for your response Joshua. It really helps to know the details of what's going on with the depletion interaction part of the code.

My supervisor got in touch with the author of the paper and I think I have a way forward now. I'm considering moving back to HoomD 2.xx and making progress from there.

Thanks
Nikhil

[Saurav Varma]

Dear Nikhil and Joshua,

I am also new to HOOMD and wanted to simulate spherocylinders with depletion interaction. I read the whole thread and had a few questions.

a) Can we simulate N_{rods}\mu_{spheres}VT ensemble in HOOMD by defining insertion and deletion moves only for one type of particle?

b) Nikhil, Why did you move to HOOMD 2.xx? Is there any advantage we have there to simulate depletion interaction?

Regards,

Saurav.