# Verified matching full-system inputs. Never append continuation/source XTCs.
topology: /Users/k20098771/Data/MD_projects/PHA/MD_data/gromacs/PHA_Enzyme/GK13_P3HO_4_gromacs/step7_production.tpr
trajectory: /Users/k20098771/Data/MD_projects/PHA/MD_data/gromacs/PHA_Enzyme/GK13_P3HO_4_gromacs/production_combined_1us.xtc
# Relative paths are resolved against this YAML's directory.
output_root: ../../../examples/output/enzyme_contacts
label: GK13–P3HO_4
protein_selection: protein
# TPR: one LIG residue (resindex 245, resid 246, seg_1_LIG), 99 atoms,
# 41 heavy atoms (32 C + 9 O). Corresponding topol.top includes toppar/LIG.itp.
pha_selection: resname LIG and segid seg_1_LIG
modes: [all_heavy, sidechain_heavy]
# Explicit inclusive window: null end means the actual final stored timestamp.
# Verified available range: 0–1480.5 ns; do not infer it from the filename.
# No equilibration period is removed and no convergence is assumed.
start_ns: 0.0
end_ns: null
# null = all stored frames (verified 0.1 ns spacing). To reduce sampling, use
# an integer multiple of the native interval, e.g. 1.0 ns.
sample_interval_ns: null
primary_cutoff_A: 4.5
extra_cutoffs_A: [4.0, 5.0]
# A small preview spread across the entire chosen window. --full disables this.
preview_frames: 31
distance_block_size: 1024