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CHILL+ Classification

CHILL+ classifies each cage-forming water molecule by its local orientational environment. It complements cage-finding methods such as TRACE: TRACE reports closed cage topology, while CHILL+ shows where ordered ice-like and hydrate-like water environments occur throughout the system.

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Structure Classes

Clavis reports six classes: The result panel reports the count and fraction of waters in every class. Use these values as a structural descriptor, not as a substitute for checking the trajectory, force field, thermodynamic state, and cage topology.

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Run CHILL+

  1. Load a structure or select a trajectory frame.
  2. Open ANALYZE and choose CHILL+.
  3. Run the current-frame analysis.
  4. Inspect the class counts, 3D colors, and classified-water network in RESULTS.
Only recognized cage-forming water residues participate in classification. Guest molecules, ions, surfactants, slabs, and other non-water residues remain ordinary scene geometry.

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3D Visualization

When analysis completes, Clavis switches the water visualization to CHILL+ class colors and draws the classified O–O neighbor network. The result controls provide:
  • HYDRATE ONLY, ICE ONLY, and SHOW ALL quick filters
  • Per-class visibility checkboxes
  • Network width and opacity controls
  • Per-class network colors or one color override
  • H-bond visibility, width, and opacity controls alongside CHILL+
CHILL+ class filtering applies only to classified water atoms. Changing the visibility, atom size, bond size, opacity, color, or render style of a non-water residue channel such as SDS or NA does not turn CHILL+ off or invalidate its water classification.
H-bonds and the CHILL+ network can be displayed together. They are separate overlays: the CHILL+ network represents the classifier’s O–O neighbor lattice, while the H-bond overlay uses the active H-bond cutoff and angular criterion.
CHILL+ visualization is preserved in path-traced output: classified oxygen colors, complete-water class filtering, non-water residues, and the classified O–O network are passed to the path-traced scene. For very large systems, begin with a 256–640 px, 64-sample GPU render because path tracing still has to construct and sample a multi-million-triangle scene.

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Trajectory Behavior

For native GROMACS and mapped LAMMPS sessions, select CHILL+ and use the trajectory range card’s Start, End, and Step values. The range action classifies those exact frames, plots the six class fractions, and exports the one-based frame labels to CSV. In-memory multi-frame GRO still uses a bounded sample of up to 40 evenly spaced frames across the full trajectory. The separate large-GRO streaming worker is not yet included in the CHILL+ sweep. When you move to another frame while CHILL+ visualization is active, Clavis refreshes the classification for the displayed frame. It preserves your class filters and network styling, but does not reuse a result whose frame identity no longer matches. Rapid native GROMACS navigation keeps the newest frame request and discards superseded requests without presenting them as runtime failures.

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Interpreting Results

  • Compare class fractions over time rather than relying on a single frame.
  • Use TRACE or another cage topology method when you need explicit cage counts and cage types.
  • Inspect interfacial classes near growth, dissociation, material, or guest boundaries.
  • Confirm that water residue names are recognized before treating a low classified fraction as a physical result.