Where are the water molecules?

[CurtisColwell]

When I run any transformation, I understand that it automatically solvates the structure. Is there a way to write out this entire system solvent and all for visualization? By default, it writes out structures with Na and Cl atoms, but no water.

Great software! It has been extremely useful!

[IAlibay]

Hi @CurtisColwell,

Apologies for the delayed response. If you want to see the whole system, you currently have to set settings.output_settings.output_indices to all instead of not water. This however will yield much larger trajectories (so you might want to adjust how often you save to frames using settings.output_settings.positions_write_frequency).

It is on our todo list to always write out a fully solvated PDB at the start of the simulation, I'll see if I can sneak that into the next release.

[CurtisColwell]

That would be great! Thanks.

I'll give this a go.