Oliver Beckstein
Oliver Beckstein
@iorga Maybe we should try out [Mike Gilson's new Bind3P water model](https://chemrxiv.org/articles/Bind3P_A_Water_Model_to_Improve_the_Accuracy_of_Binding_Calculations/5848113)? They tested it with host-guest but perhaps it also works better for solvation free energies See also #81...
@ianmkenney said he doesn't want to maintain [pybol](https://github.com/ianmkenney/PyBOL) anymore so we need to replace it with something simpler. EDIT: ~*Maybe* this helps with the strange errors on CI, where templates...
The `scripts/mdpow-*` scripts are not tested at all. - [ ] run scripts with simple input and _short_ run time in at least the lowest and highest python-version - [...
mdpow still uses some constants like kBOLTZ and N_AVOGADRO. Replace with using scipy.constants
At the moment we use GromacsWrapper's [numkit.observables](http://gromacswrapper.readthedocs.io/en/latest/numkit/observables.html) to represent results, mainly to do error propagation. However, there's the mature https://github.com/python-quantities/python-quantities (which even comes with proper unit support) and we should...
https://alchemlyb.readthedocs.io/en/latest/visualisation.html should be used for the scripts
We need a way that the Pcw and Pow calculations can use water runs that were not originally part of the same MDPOW run (not in the same directory). Perhaps...
At the moment (after #31), MD_NPT runs with Parrinello-Rahman barostat (and Langevin thermostat) but the FEP windows (with the same thermostat and barostat) regenerate velocities. We can consider using continuation...
Standard ions should be supported in the aqueous phase - [ ] NaCl - [ ] KCl It should be possible to set the concentration in the input file.
The new propka 3.2.0 release breaks the internal API in parts. To check - run.single() still works - getting the information from the molecular container still works - increase minimum...