Lester Hedges

I've now added some functionality that you can do static analysis of an existing simulation using `BioSimSpace.FreeEnergy.analyse(work_dir)`. It will figure out everything from the information in the `work_dir`, i.e. the...

I've added another update when so `getData` is static so you can use it on an existing working directory without needing to instantiate another `FreeEnergy` object. (N.B. The Sire macOS...

This is a good question. I was hoping that we could use `devel` once I've merged the Exscientia ABFE PR, with (some) of the FEP part using the Sandpit, rather...

Thanks, @noahharrison64. I'll take a look. The code just adjusts the `mass` property, so I'll see how this is used by the AMBER topology parser. It may be pre-filling some...

(Sorry, meant to say the GROMACS topology parser.)

Yes, the mass is coming from the mass of the element, which isn't modified. I think this is okay, though, since the mass in the `[atoms]` section takes precedence. For...

Hi there, It's hard to say, but it certainly wouldn't hurt to try. I could certainly imagine that HMR might cause issues if the system was poorly equilibrated to begin...

What do the trajectories look like when they crash? Are there any weird fluctuations or steric clashes?

Potentially you should be able to resolvate a system that was previously solvated and specify a new ion concentration. This would keep all existing water molecules, then adjust the ion...

Ah, I see. We currently don't provide support for membrane simulations. This is a know issue with `gmx solvate` (our solvation backend) and they describe the issue, and some suggested...