Run_Multi-Part_Simulation.bash is in two places

[gitoliver]

The file here:
https://github.com/GLYCAM-Web/MD_Utils/blob/actual/protocols/Glycan/Prep_and_Minimization/Run_Multi-Part_Simulation.bash
Is different than from here:
https://github.com/GLYCAM-Web/MD_Utils/blob/actual/scripts/Run_Multi-Part_Simulation.bash
I assume from how they are written that they are meant to be used by any protocol. Not that Roe has one of these, and Glycan the other. Note that the one being used by Glycan tries to use functions that only exist in the other one, for example these are always happening in Minimize.log:
Run_Multi-Part_Simulation.bash: line 169: print_to_details_log: command not found
Run_Multi-Part_Simulation.bash: line 170: print_to_details_log: command not found

[Lachele]

The one in the protocols dir is a symbolic link to the other. Eventually, the one in the scripts dir will be used for various protocols.

The one in Glycan is old. I've been meaning to update that protocol to use the new version. I will look at the one in Glycan. It was the first one that was written, so it certainly used to have those functions.

[Lachele]

I take it back... I think those lines were added to the Glycan version when we implemented nstlim-setting for testing workflows. I will fix it.