# GK13-P3HO_4: trajectory preparation
#
# RUN FROM THIS analysis FOLDER:
#   bash process_trajectory.sh
#
# OPTIONAL CHECK (does not process or write trajectories):
#   bash process_trajectory.sh --dry-run
#
# The script reads the settings below each time you run it.
# Edit values after =, save this file, then run the command above.
# Use plain values without quotes, spaces around =, or inline comments.
# Relative paths are resolved from this analysis folder.
#
# Workflow:
# 1. The combined raw XTC stays in the parent simulation folder.
# 2. All frames are centred on SOLU and compact-wrapped with -pbc mol.
#    SYSTEM is retained, including water and ions. No fitting is applied.
# 3. Every 100th processed frame is saved separately for VMD.
#
# ANALYSIS: use processed.xtc. In MDAnalysis, u.trajectory[::100]
# samples every 100th frame without changing the stored file.
# Enzyme-PHA distance/contact calculations must still account for PBC.
#
# VMD: load step6.2_npt.gro, then add processed_every100.xtc to that molecule.
# Use a GRO with the same atoms and ordering as the production TPR/XTC.
#
# Existing outputs are protected. To rerun, rename earlier outputs or set
# new PROCESSED and PREVIEW filenames below. If a run fails, inspect any
# partial output before deciding whether to rename or remove it.
#
# Requires GROMACS (gmx) in your active terminal environment.
# No iPHASimulator package, Python, or notebook is needed for this script.
# This is plain KEY=value data, not YAML; do not pass it to a Python YAML loader.
# Retain the full system in OUTPUT_GROUP so the original TPR/index also match
# processed.xtc in the second command. Do not select a solute-only subset here.

INPUT=../production_combined_1us.xtc
TPR=step7_production.tpr
INDEX=index.ndx
CENTER_GROUP=SOLU
OUTPUT_GROUP=SYSTEM
STRIDE=100
PROCESSED=processed.xtc
PREVIEW=processed_every100.xtc
GMX=gmx