tutorials for polymer/protein/rna structure simulations

[Olivia Viessmann]

Hi, 
I just started with HOOMD and am interested to simulate polymer/protein/RNA like structures. Is anyone aware of tutorials out there that use HOOMD to simulate these objects? Anything vaguely towards that direction would be greatly appreciated. 

Many thanks

Olivia

[Brandon Butler]

Hi Olivia,

See the tutorials on MD (https://hoomd-blue.readthedocs.io/en/latest/tutorial/01-Introducing-Molecular-Dynamics/00-index.html) and the how-to in simulating molecular systems (https://hoomd-blue.readthedocs.io/en/latest/howto/molecular.html).

Best,

Brandon

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[Olivia Viessmann]

Hi,

Thank you for the reply. I am particularly interested in the init.create_random_polymers()

Function that seemed to be available in the hoomd v2 versions. Is there an equivalent in the newer v3 version of hoomd?

I am struggling to figure out how to create a polymer chain from the MD simulation tutorials.

Thanks

Olivia

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[Brandon Butler]

No there is no such function. Feel free to use Python packages like mbuild to construct polymers. For use see their documentation https://mbuild.mosdef.org/en/stable/index.html.

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[Olivia Viessmann]

Hi Brandon,

Thanks for the links. Are you aware of any minimally working example code of a polymer using hoomd v3 that I could start with?

Thanks a ton

Olivia

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[Jakin Delony]

I had a similar issue in v3 and wrote a small initial configuration generation script for linear homopolymer systems that's attached here.  There are a few caveats, though.  The initial configuration is a naive linear polymer built on a lattice (think pencils in a box) and will require longer relaxation times because the initial state is not very realistic.  Also, in its current form it does not account for complexities such as branching, cross-linking, or copolymerization.  All it does is extend the particle, bond, and angle initialization routine in the tutorial to account for arbitrary chain length (DOP) and number of chains (num_chains).

Hope this helps,
Jakin

[Joshua Anderson]

Olivia,

The minimal working example was the 2nd link that Brandon sent you: https://hoomd-blue.readthedocs.io/en/latest/howto/molecular.html
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

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> <gen_lattice_polymer.py>

[Olivia Viessmann]

Thank you everyone for the input. This is very, very appreciated and super helpful. 

Olivia

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