Lester Hedges

I'll try to test this later. I see that there are multiple `process.getSystem()` calls in your script. Are they all failing, or just the final one for equilibration? I see...

Just tested a shorter CPU simulation of 0.01 nanoseconds and it works for me, i.e. I don't get any errors and there are `equilibrated.*` files in my working directory. Could...

> I've abandoned the protein PDB that was causing the issues and chose another one. Yes, this is rather weird. Trust us to choose a system that misbehaves! I did...

I wonder if there's a rounding issue with the way I compute the fraction of the trajectory that has completed in order to work out the current frame when you...

Yes, I think that's the issue. It is caught as an exception in `getFrame`, but in `getSystem` I use a `try/except` block since you don't want it to fail when...

Hi there, No you're not missing anything. The issue is providing the user with the flexibility of running a _single_ lambda window, e.g: ```python protocol = BSS.Protocol.FreeEnergy(lambda=0) # Run a...

This is a hack for quickly setting up multiple processes that happen to share an identical input system, differing only by a single entry in their configuration file. If you...

Yes, I see, that wasn't a consideration at the time. I imagine this hack can be consumed into `BioSimSpace.Process`, i.e. by adding some hidden functionality to clone a process and...

Hi there, as @jmichel80 says we currently use monatomic ions for solvation and allow the user to specify consistent ion parameters when parameterising in the presence of structural ions. Please...

Hi there, It appears that it works if you use the _original_ PDB file, but not the one written by BioSimSpace (using its internal PDB parser) during the parameterisation. Looking...