Bas Rustenburg
Bas Rustenburg
Brainstorming things to do before we can start using this code more reliably. Tagging @jchodera @gregoryross, feel free to add points by editing (assuming you can) or replying. - [x]...
The new openmmtools integrators have some new getter functions that we may want to use inside of the ncmc protocol work method.
The `remove_temp_files` keyword argument under `protons.ligands.generate_protons_ffxml` appears to be broken. Some files can not be removed because they are still open at the time of deletion. Recommended workaround right now...
At some point in the future, we should come up with a preferred way of dealing with atom types. For now, a low priority since we have a working solution....
This is a reminder of the slow parts of __init__, in case we ever want to speed it up. We may be able to cache some exception parameters instead of...
We should add support for custom forces. the parameter names used in software such as Yank should have been standardized. We can adhere to the same standard in the code...
The titration state weight is assumed to be in units of molar energy: https://github.com/choderalab/protons/blob/master/protons/driver.py#L515 If you store the numbers obtained directly from calibration, this would give you beta^2 * g_k....
As a reminder to do some debugging, I'm logging some simulations that failed, in case the issues are related to the code. Failed simulations that will need debugging. - ./ALK-Alectinib/3AOX_fixed_ph7.4.pdb.ligand/failed.txt...
Document how to use tleap, and cpin_util.py to start a constph simulation.
I had a few thoughts on implementing the two-step method from the Chen&Roux paper. (doi: 10.1021/acs.jctc.5b00261), and I just wanted to leave those here to make sure I am interpreting...