Inexact Error: trunc(Int64, NaN) when running example 6 steepest descent

[kool7d]

Inexact Error: trunc(Int64, NaN) when running example 6 steepest descent

[JosePereiraUA]

So, this was an interesting one.
I actually found 2 problems:

1. So, the first one was actually on the recovery from previous steps. The copy function was being used instead of ProtoSyn.recoverfrom! (which makes sure the pose graph and state ids remain connected). I'm not sure but I think somehow this is what was causing the GB problem.

2. The second one was a wrong negative sign when calculating forces in the distance-based flat-bottom potential restraint employed in the "all-atom clash restraint" component. Atoms were actually being pushed together instead of further apart.

All-in-all, the two fixes I've added should solve this issue. I've also went ahead and refurbished example 4. Take a look at commit 985e098, and give me some feedback.

[JosePereiraUA]

Seems like this issue has been resolved. Closing.