Lester Hedges

Just to note that the BioSimSpace System object has a `getIndex` method that can take objects that it contains, e.g. molecules, atoms, residues, and return the _absolute_ index of that...

Hi there, Yes, at the moment there is no way to specify the GPU platform in the FreeEnergy class since it wouldn't be consistent between the MD engines that we...

Hi Sofia, Could you activate verbose mode in BioSimSpace to see what the Sire error is? See here for details: https://github.com/michellab/BioSimSpace/issues/137 I might have some time later too take a...

Ho @SofiaBariami. Your link doesn't contain the two files `G1_4a.prm7` and `G1_4a.rst7` so I can't fully test the performance issue that you describe. However, I've simply tried loading the two...

You can check that a molecule has a particular property by using, e.g. `mol._sire_object.hasProperty("property")`. Your `decouple` function could delete the property (using `.removeProperty` on an editable version of the molecule,...

Yes, `is_perturbable` is widely used and is, for example, also checked for the the Sire GROMACS topology parser. Without knowing more about things I don't know if _decoupled_ is distinct...

Thanks, this sounds great. I should be able to take a look through the code early next week and will get back to you with any comments / suggestions.

Thanks again for this, it will be a really useful feature. I was wondering if we could assign a _variable name_ to each collective variable to simplify the creation of...

Hi there, I would prefer if we set HMR as an option at the protocol level, (This could be added to any protocol where we'd like to support HMR.) We...

There would also be some redundancy, since an appropriate time step would also need to be chosen. I guess HMR could be activated by default (with default options) whenever a...