Scientific assumptions

SAMMD builds deterministic self-assembled monolayer systems and exports OpenFF Interchange artifacts for OpenMM handoff. These assumptions describe what that build means physically and what remains outside SAMMD’s ownership in this release.

Surface and SAM placement

SAMMD uses registered Fcc(111) metal surfaces, defaulting to Pd(111). The slab is centered at the origin, with SAMs placed normal to the surface: +z for the top face and -z for the bottom face.

The hollow-site placement strategy is an internal fcc_hollow default. SAMMD selects sulfur pairs to the three nearest hollow-site metal atoms for each placed thiol anchor. Beginner YAML input does not expose adsorption-site selection in this release.

Beginner SAM inputs should be neutral thiols with an HS/implicit-H thiol sulfur, not pre-deprotonated thiolates. SAMMD uses the sulfur atom for placement while keeping the beginner chemistry description neutral.

Box planning

Padding is measured from the fully extended SAM tips to the box boundary. This keeps the requested spacing tied to the longest planned SAM conformation rather than only to the metal slab.

Force-field assumptions

Base metal Lennard-Jones parameters come from the INTERFACE Fcc metal data. The target route for organic molecules is OpenFF, and sammd build exports the OpenFF/OpenMM-ready system artifacts for supported non-salt configs.

The selected metal-S Lennard-Jones override is an internal, post-export proxy for a tunable strengthened nonbonded interaction. It is not covalent, quantum, or reactive chemisorption, and it is not currently a beginner YAML knob.

Simulation boundary

SAMMD does not own minimization, equilibration, production, trajectory writing, or reporter setup. Those OpenMM simulation protocol choices are handled in separate scripts or future teaching material after system construction artifacts exist.