Lester Hedges

I've pushed some changes to the [feature_steered_md](https://github.com/michellab/BioSimSpace/tree/feature_steered_md) branch. Here I've implemented an RMSD collective variable that can be used for metadynamics simulations as well as steered MD, although I've yet...

Let me know if the constraints are too stringent, e.g. if we want to be able to handle reference molecules that have atoms that aren't in the system. (This is...

I'm also not sure whether it's best to specify the atoms that are involved in the RMSD calculation by index, or to use the residue index as you have done....

Also, do we need any special handling for the case were all atoms in the reference are used for the RMSD, e.g. should both the occupancy and beta values be...

I've now created a `BioSimSpace.Protocol.Steering` class that can be used to set up a schedule for performing steered MD. I just need to convert this to the correct PLUMED file...

For simplicity I've decided to leave the RMSD CV _as is_ for now. It should work for the purposes of the steered MD (assuming that inputs are edited so that...

With regards to output from PLUMED when running steered MD: It looks like you can just print exactly the same information as you would when running metadynamics, i.e. the time...

I've now got steered MD working with GROMACS in the [feature_steered_md](https://github.com/michellab/BioSimSpace/tree/feature_steered_md) branch. I'll test it with your example input (I'll tweak the reference file to only include the atoms in...

The expectation is: 1) The reference can be matched to a single molecule in the system. (If the user passes an index, then this is clearly unambiguous.) 2) All atoms...

Atoms are matched by residue number and name, so the ordering within a residue can be different, or atoms missing from within a residue, i.e. heavy atoms only.