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TorchMD Autodiff Example

Introduction

This example demonstrates the benefits of automatic differentiation within a molecular dynamics engine. We first simulate a waterbox and frequently save the coordinates and velocities. Then we try to infer the force field parameters from this trajectory.

Requirements

  • torchmd
  • tqdm
  • torch (tested with version 1.4.0)
  • numpy
  • matplotlib

Scripts and Files

  • waterbox.py -- Definition of the molecular system based on files in the torchmd test suite.
  • simulate.ipynb -- Jupyter notebook for simulating the water box.
  • learn.ipynb -- Jupyter notebook for learning the parameters from the trajectory.
  • integrator.py -- A version of the torchmd integrator without inplace operations
  • plot.ipynb -- plotting script
  • writeup.ipyng -- for the paper