I ran 3D Flex with default parameters except for using 32 layers. I used 32 layers because my protein is relatively small (~250 kDa). I have very different plots from the tutorial video. What parameters should be first tuned to get better training results?
I am having the same issue with the top left graph- everything is lumped into one line and I don’t know why. It made me worry there would be no results, but I actually did get some decent results.
It looks like you may need to play around with some of the parameters such as the noise injection standard deviation and the latent centering strength to fix the bottom left “flow generator” graph. Maybe relaxing the rigidity might help as well. Once all of that is optimized, the “Relative change of loss and penalty” graph might improve.