Alexander Matthew Payne

Hi @d-beltran , so sorry for the delay on this! The responsibility of maintaining MDTraj has been transitioning (more info to come soon!). Did you resolve this issue or is...

Right, that looks like somewhat a logical fix (enforcing the angles). What are you using to run your simulations? I don't understand how you could have `unitcell_lengths` of 0

Hi @mrjoness, so sorry for the delay on this! The responsibility of maintaining MDTraj has been transitioning (more info to come soon!). Have you figured out how to do this?

please send a complete code snippet! What are the CA atoms in DNA? DNA does not have alpha carbons (at least not in the way we mean them in proteins)....

Also experiencing this!

I think @sukritsingh will be adding some examples using collective variables? happy to help with those

this exists, no? https://github.com/openmm/openmm-cookbook/blob/main/notebooks/cookbook/Restraining%20Atom%20Positions.ipynb

@peastman @sef43 @jchodera I'd like to finally fix the issues with the B2AR tutorial, which is in: notebooks/tutorials/Beta_2_adrenergic_receptor_B2AR_membrane_protein_simulation_with_CHARMM.ipynb This would potentially close some previous issues, linked here: - https://github.com/openmm/openmm/issues/3152 -...

Great, thank you both! > How large are the files? If they're fairly small we can just include them in the repository. If they're larger we may want to find...

> Is there somewhere else we could put them? I don't know if I'm the person to answer this question? I guess wherever this is hosted: https://openmm.org/tutorials_/b2ar_membrane/files/charmm-gui.zip EDIT: https://github.com/openmm/openmm-org/tree/master/tutorials_/b2ar_membrane/files I...