We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of statistical physics simulation environments as well as interaction potentials and neural networks that can be integrated into these environments without writing any additional code. Since the simulations themselves are differentiable functions, entire trajectories can be differentiated to perform meta-optimization. These features are built on primitive operations, such as spatial partitioning, that allow simulations to scale to hundreds-of-thousands of particles on a single GPU. These primitives are flexible enough that they can be used to scale up workloads outside of molecular dynamics.

All reviewers agree that this paper describes a technically impressive contribution to machine learning research. Although the field of "physics and ML" is relatively small, it is growing, and the techniques underpinning this work offer clear learnings for the wider ML community. Therefore, it appears clear that the audience for this paper is the NeurIPS audience, and the level of contribution is at the level of NeurIPS papers. All reviewers, and R3 in particular had some questions about the style of presentation, and I am content with the rebuttal's statement that the authors will take the feedback on style for a final version.

We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of statistical physics simulation environments as well as interaction potentials and neural networks that can be integrated into these environments without writing any additional code. Since the simulations themselves are differentiable functions, entire trajectories can be differentiated to perform meta-optimization. These features are built on primitive operations, such as spatial partitioning, that allow simulations to scale to hundreds-of-thousands of particles on a single GPU. These primitives are flexible enough that they can be used to scale up workloads outside of molecular dynamics.

A large fraction of computational science involves simulating the dynamics of particles that interact via pairwise or many-body interactions. These simulations, called Molecular Dynamics (MD), span a vast range of subjects from physics and materials science to biochemistry and drug discovery. Most MD software involves significant use of handwritten derivatives and code reuse across C++, FORTRAN, and CUDA. This is reminiscent of the state of machine learning before automatic differentiation became popular. In this work we bring the substantial advances in software that have taken place in machine learning to MD with JAX, M.D. (JAX MD). JAX MD is an end-to-end differentiable MD package written entirely in Python that can be just-in-time compiled to CPU, GPU, or TPU. JAX MD allows researchers to iterate extremely quickly and lets researchers easily incorporate machine learning models into their workflows. Finally, since all of the simulation code is written in Python, researchers can have unprecedented flexibility in setting up experiments without having to edit any low-level C++ or CUDA code. In addition to making existing workloads easier, JAX MD allows researchers to take derivatives through whole-simulations as well as seamlessly incorporate neural networks into simulations. This paper explores the architecture of JAX MD and its capabilities through several vignettes. Code is available at www.github.com/google/jax-md. We also provide an interactive Colab notebook that goes through all of the experiments discussed in the paper.