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Towards Conditional Generation of Minimal Action Potential Pathways for Molecular Dynamics. (arXiv:2111.14053v2 [q-bio.BM] UPDATED)
Jan. 7, 2022, 2:10 a.m. | John Kevin Cava, John Vant, Nicholas Ho, Ankita Shukla, Pavan Turaga, Ross Maciejewski, Abhishek Singharoy
cs.LG updates on arXiv.org arxiv.org
In this paper, we utilized generative models, and reformulate it for problems
in molecular dynamics (MD) simulation, by introducing an MD potential energy
component to our generative model. By incorporating potential energy as
calculated from TorchMD into a conditional generative framework, we attempt to
construct a low-potential energy route of transformation between the
helix~$\rightarrow$~coil structures of a protein. We show how to add an
additional loss function to conditional generative models, motivated by
potential energy of molecular configurations, and also …
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