Lester Hedges

Just added some comments. This is still a WIP so I'll add more if I think of anything. Thanks again for this. It will be good to catch up after...

Hi @jmichel80. Yes, this would certainly be a desirable feature. I think our original aim was the ability to re-initialise a `FreeEnergy` object by passing an existing working directory to...

Thanks, @AdeleLip, that's really useful. I'll see what's possible to re-implement within BioSimSpace. FYI: I've just pushed an update that adds a `.getFrame` method to all `BioSimSpace.Process` classes. This allows...

Yes, most functionality for doing this already exists in BioSimSpace so I'll cook up an example tomorrow. Do you have example input files for the system and target (RMSD reference)...

Thanks for the detailed explanation. For the example files that you provided there are residues in the target PDB that aren't found in the system. Using the Sire/BioSimSpace search functionality...

Okay, [here](https://github.com/michellab/BioSimSpace/files/6172706/rmsd_test.tar.gz) is an archive containing a hokey script that uses Sire/BioSimSpace to create a PDB file for PLUMED. Just run `test.py` in the extracted directory, which should create a...

Note that if we don't need additional info in the PDB file, e.g. `MODEL` and `CONECT` records, then we can use `Sire.IO.PDB2` directly and strip these from the output.

Ah brilliant, thanks for the clarification, I thought I was missing something obvious ;-) I had also assumed that _all_ atoms in the target PDB that appear in the system...

Sorry for the slow update on this. I realised the steered-MD is generic to any collective variable supported by PLUMED, with targeted MD (using RMSD as the target) being a...

Ah, perfect. I actually thought I had opened the _reference_ file but my terminal autocomplete must have filled in _renumbered_ instead when I hit tab. Bah :facepalm: