Lester Hedges

This is now fixed. There were some issues with formatting for combining searches via a logical `and`. We also no longer need to do searches like `atoms in ...` since...

Well, it took all of a day for the next set of issues: * In the change from version 4.0.1 to 4.0.2 of openmpi-mpicc (which is used to compile GROMACS...

Hi @SofiaBariami, I was online and happened to have a spare few minutes so took a quick look at this. For reference, this is how you can see the full...

I didn't try reading the PDB file that Sofia uploaded, the issue was with the prm7/rst7 files generated by Parmed. As mentioned previously, we don't rely on CONECT records since...

Thanks, @jmichel80. You are correct, we currently need to know the water topology in order to re-solvate the system for the free leg of a binding free energy simulation. I...

I currently guess the water model topology if the information is missing in [free_energy.py](https://github.com/michellab/BioSimSpace/blob/devel/python/BioSimSpace/FreeEnergy/_free_energy.py). For now, I'll add the same logic to the binding free energy code and warn the...

I have pushed a workaround for your issue which should work in most cases. The only thing I don't account for is detecting SPC/E rather than TIP3P. You should no...

Hi @jmichel80, is this workaround satisfactory for your use case? Assuming you'd like to solvate in one BioSimSpace node, then setup an FEP simulation in another, then BioSimSpace would correctly...

Yes, it could just be an additional record in the YAML file that is already created by a node.

GROMACS will happily solvate around existing water molecules in a system, although it wont convert these molecules to match the topology or naming scheme of the chosen water model. This...