Generative Modeling of Molecular Dynamics Trajectories
This work addresses computational bottlenecks in molecular dynamics for researchers in computational chemistry and biophysics, offering a flexible multi-task surrogate model.
The paper tackles the high computational cost of molecular dynamics (MD) by introducing a generative modeling approach for molecular trajectories, enabling tasks like forward simulation and transition path sampling, and demonstrates its capabilities on tetrapeptide simulations and protein monomers.
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.