protein folding and structure prediction. Protein simulations typically define an energy function, similar to a loss function, over all the atoms in the protein. There are many terms: at least one per bonded atom pair, at least one per bonded atom triple, at least one per bonded atom quadruple, one per each non-bonded pair (although atoms that are distant can be excluded, sometimes making this a sparse matrix). If you start with a proposed model (say, random coordinates for all the atoms) and apply gradient descent, you'll end up with a mess. All those energy terms end up creating a high dimensional surface that is absurdly spiky in the details, and extremely wavy with many local minima at coarse grain.

Instead of using gradient descent, we used molecular dynamics (I'm unaware if this has a direct equivalent) to sample the space by moving along various isocontours (constant energy, or constant temp, or usually constant pressure). Even so, you have to do a lot of sampling- in my day, it was years of computer time, now it's months- to get a good approximation to the total landscape, and measure transition frequencies between areas of the landscape that correspond to energy barries (local maxima) that are smaller than the thermal energy avaialble to the system.

It's complicated. also, deep mind obviated all my work by providng that sequence data (which is cheap to obtain) can be used to predict very accurate structures with little or no simulation.