AdeleHardie

So would the variable names be `cv0, cv1, ...` in the order they appear in when the CV objects are being passed? And the expression would then be validated and...

I have started testing GROMACS+PLUMED for steered MD [here](https://github.com/michellab/PTP1Bfrags/tree/main/gromacs). I looked at `BioSimSpace.Metadynamics.CollectiveVariable` and the only available ones at the moment are distance, funnel and torsion. So for now I...

Following today's discussion, I'm linking the functions I use to prepare input PLUMED files for steered MD. `renumber_pdb()` and `rmsd_reference()` [here](https://github.com/michellab/PTP1Bfrags/blob/main/scripts/reference_files.py) are used to prepare the reference PDB structure, and...

Yes I've adjusted the trajectory analysis notebook to use `getFrame()` and it works great for extracting snapshots. [Here](https://github.com/michellab/BioSimSpace/files/6166344/rmsd_files.zip) are some example input files. The system files are just results of...

In this case the target protein (WPD loop closed) sequence is a bit longer than the system (WPD loop open) since the C terminus of the WPD loop open is...

I have now added some more tutorial background in the [setup-sMD notebook](https://github.com/michellab/PTP1Bfrags/blob/main/gromacs/setup-sMD.ipynb). Some of it is subject to change depending on what you decide to implement in BSS, but it...

I think the problem at the moment is the beta and occupancy columns - with how they are now, PLUMED will use the atoms that do not exist in the...

In my experience the RMSD residues have always been continuous, but I'm not sure if that would always be the case. Most other libraries I have used let you give...

You are looking at `renumbered.pdb` which only has adjustments made to the atom index. The actual file used by PLUMED (should be in the PLUMED example file) is `reference.pdb`, where...

About specifying atoms vs whole residues - I think atom indices are the way to go. In my case I use all heavy atoms and the reference PDB does not...