WTMetaD simulation of alanine dipeptide with deep-TICA collective variables.

WTMetaD:

A. Barducci, G. Bussi, and M. Parrinello, ``Well-tempered metadynamics: A smoothly converging and tunable free-energy method,'' Phys. Rev. Lett., 100, 020603 (2008)

Deep TICA:

W. Chen, H. Sidky, and A. L. Ferguson, ``Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets,'' J. Chem. Phys., 150, 214114 (2019)

OpenMM:

Networks are created and trained with PyTorch: https://pytorch.org/

Simulations are done using OpenMM https://openmm.org/

with bias forces implemented by the PyTorch plugin: https://github.com/openmm/openmm-torch

and converted to a TorchScript module. The conda environment is described in openmm-torch.yml.