  Variational auto-encoder frameworks have demonstrated success in reducing
complex nonlinear dynamics in molecular simulation to a single non-linear
embedding. In this work, we illustrate how this non-linear latent embedding can
be used as a collective variable for enhanced sampling, and present a simple
modification that allows us to rapidly perform sampling in multiple related
systems. We first demonstrate our method is able to describe the effects of
force field changes in capped alanine dipeptide after learning a model using
AMBER99. We further provide a simple extension to variational dynamics encoders
that allows the model to be trained in a more efficient manner on larger
systems by encoding the outputs of a linear transformation using time-structure
based independent component analysis (tICA). Using this technique, we show how
such a model trained for one protein, the WW domain, can efficiently be
transferred to perform enhanced sampling on a related mutant protein, the GTT
mutation. This method shows promise for its ability to rapidly sample related
systems using a single transferable collective variable and is generally
applicable to sets of related simulations, enabling us to probe the effects of
variation in increasingly large systems of biophysical interest.
