build

Compute total system charge from actual residue counts in the universe.

This is needed because transformations like sphere cropping or shell projection may change residue counts from the input specification.

Get the parametrization function, optionally wrapping with config for SMIRNOFF.

Build a mixed-box system: compress, ionize, write topology and run files.

Create a mixed-box universe by packing at low density then compressing with OpenMM.

Build a bilayer system: compress, solvate, ionize, write topology and run files.

Create a bilayer universe by placing lipids then compressing with OpenMM.

Build an LNP (Lipid Nanoparticle) system.

The LNP consists of:

• Core (internal): A compressed sphere of lipid molecules
• Shell (external): A spherical monolayer wrapping the core

Workflow:

1. Create core via create_mixedbox_by_compression → create_sphere
2. Create shell via create_bilayer_by_compression → shell_from_monolayer
3. Merge core and shell components
4. Solvate with spherical exclusion zone
5. Ionize the solvated system
6. Write topology and run files

Create the LNP core by compressing a mixed box and shaping into a sphere.

For efficiency, we pack only a unit cell (1/n³ of total molecules) and replicate it n×n×n times before cropping to a sphere.

Create the LNP shell from a monolayer projected onto the core surface.

Log a table comparing input fractions vs actual fractions for core and shell.

Merge core and shell into a single LNP universe.

The shell is positioned around the core and the combined system undergoes a brief equilibration with spherical restraints.

Add ions for neutralization and salt concentration.