# Config-driven iPHASimulator v2 validation workflow.
#
# This file is intended for script and HPC runs. Start with small systems and
# fast gas charges, then switch charge_method to abcg2 (default) or bcc for more realistic GAFF2
# charge assignment after the workflow is stable.

output_root: examples/output

targets:
  - monomer: 3HB
    degree: 4
    stereochemistry: R
  - monomer: 3HO
    degree: 4
    stereochemistry: R
  - monomer: 3HDD
    degree: 4
    stereochemistry: R

stages:
  build: true
  gaff2: true
  openmm: true

gaff2:
  charge_method: gas
  net_charge: 0
  residue_name: PHA
  atom_count_warning_threshold: 120

openmm:
  minimization_max_iterations: 200
  nvt_steps: 100
  npt_steps: 100
  production_steps: 100
  report_interval: 10
  temperature_kelvin: 300.0
  pressure_bar: 1.0
  platform_name:
  platform_precision: mixed

slurm:
  job_name: ipha_validation
  time: "02:00:00"
  partition: standard
  cpus_per_task: 4
  mem: 8G
  conda_env: ipha