Lester Hedges

Fantastic, thanks for these. I'll try to incorporate the changes tomorrow morning and report on progress during the meeting. For simplicity I'll probably bundle your modified metadynamics script and copy...

Okay, I think I've updated our OpenMM metadynamics driver to add the implementation for your PLUMED compatible HILLS file. Could you take a look at the `openmm.py` script that is...

We might also need to write the OpenMM colvar to a text file, but that should be easy enough to do, or check for the `COLVAR.npy` file and convert it...

Thanks, I'm glad that the FES agree with OpenMM :+1: I'll run the HILLS file through our own `sum_hills` wrapper when I get a chance to make sure all is...

Was the system completely prepared in BIoSimSpace, or was this a fully solvated system that you loaded in initially? If the latter, could you upload those files too. We do...

Running the minimisation with GROMACS (using the solvated system directly) works so something must be going wrong with the conversion to AMBER, which is what is used for OpenMM. I'll...

Actually, we don't convert the water topology when running with OpenMM, only with AMBER or GROMACS. This means that OpenMM is using AMBER format files with a GROMACS water topology....

I think it's an issue with the protein. If I just solvate the protein, I see the same blow up. If I just solvate the ligand, then it works.

For reference, the minimisation crashes if you just use the protein in vacuum, so I don't think it's anything specifically to do with the water molecules in the system.

> Running the minimisation with GROMACS (using the solvated system directly) works so something must be going wrong with the conversion to AMBER, which is what is used for OpenMM....