msultan

Also make sure that the output of the network matches the output from pytorch. They should match up to 4 sig figs at least

ahh good catch with the ```index```, I think it ended up not too much of an issue because I switched towards called in input [features layer](https://github.com/msultan/vde_metadynamics/blob/master/examples/ww_domain/ww_domain_mdl_train_and_plumed_file.ipynb) (cell number [65] )...

if you are done with the PR, i can merge the changes. Thanks for bringing these in, I really appreciate it.

@cxhernandez can speak to this more but my guess is that a directed graph would double the number of edges and would likely look very messy. For your side question,...

+1 for getting this done somehow at least . I always forget to do this properly and it would be nice to automate it. I was thinking maybe a super...

@cing Or you know just use ```kinase_msm``` 😄 , 😆

errorbars, movie makers