Closed xiki-tempula closed 2 years ago
Would there be a situation where you want to simulate lone water molecule in vacuum? I can certainly check for water molecules and do the conversion in all cases, but just wanted to check if this was a situation that someone would come across in practice? (That said, I imagine there could be issues if crystal waters were present, but that's an issue for another time.)
@lohedges I think this is more like how one organise the code and where should the system._set_water_topology
be called.
Do we expect the everything (topology and beyond) to be modified based whether this is in vacuum or not. Or the only difference between the in vacuum or not is strictly the box size and the cutoff.
Ah, I see the issue. While set_water_topology
is called at the start of the setup, i.e. before any protocol specific configuration things are implemented, the original system (without modified water topology) is used to write the modified gro
file, which is needed in the case of vacuum simulations, i.e. to add an infinite periodic box. This problem is specific to GROMACS.
I'll fix this when I get a moment.
Thanks for catching!
Prerequisites
This might be an edge case as I'm lazy and find this issue when trying to scavenge some of the existing test.
So the water name is