Sander Roet

easiest way I found by running (assuming a limited set of molecules) for each molecule ```python import mdtraj as md traj = md.load("1vii_3frames.pdb") com = md.compute_center_of_mass(traj, select="protein") # change the...

# Important things to keep in mind with atom_slice **always** give a unique and ordered list to `atom_slice`, otherwise you run into issues like #1664 . Also, after `atom_slice` the...

that specific error during compilation seems to be with compiling numpy from source? ``` Building wheels for collected packages: numpy Building wheel for numpy (setup.py): started Building wheel for numpy...

> @sroet , what do you think? One straightforward fix would possibly be editing I have no strong preference either way, as long as a consistent file is written (which...

@mizimmer90 The maintainers of this codebase seems quite willing to look at PRs, so feel free to open one if you have the time and need. If you do decide...

I do not use this personally, so no strong opinion either way. I did have a small remark on the proposal: > Checkpoint trajectory: One xtc file per replica. You...

> I'm a bit surprised to see such hard pinning, I personally prefer adding lower constraints until it's known that an upper constraint is also needed. The reason for these...

> Or, maybe we should use https://github.com/scipy/oldest-supported-numpy like sklearn does. This looks like a good solution for everyone. The current implementation was based on the `scipy` implementation at the time,...

I ran into the same bug today (also with `model_angelo refine` and with the same error). (Just leaving a comment to confirm it is probably not model/map specific and to...

+1 on the rename, feel free to do it whenever you want. Sure, I can run through the instructions once you decide to run it. I think I remembered that...