Make solute-only trajectory writing optional
jchodera opened this issue · comments
Typical calculations generate NetCDF files that take up way too much space.
For example, a typical SARS-CoV-2 Mpro calculation will generate a positions variable in the complex NetCDF file that consumes (18 replicas) (5000 iterations/replica) (10000 atoms) (3 dimensions/atom) (4 bytes/dimension) = 10GB of data.
Instead, we should default to setting atom_selection = None (or perhaps an empty list, depending on what the multistate sampler expects) and suggesting our examples remove atom_selection: not water from the input YAML.
We can still extract some useful analysis out of the checkpoints as needed.
Changing the default value to none in
We probably want to delete the atom selection from the examples.
