The Configuration File

The complete pSTY.yaml file written by 1-polystyrene.sh is shown below. A detailed explanation of every directive appears in the configuration-file reference.

Title: polystyrene
gromacs:
  gmx: gmx
  gmx_options: -quiet -nobackup
  mdrun: gmx mdrun
  mdrun_options:
    gpu_id: 0
ambertools:
  charge_method: gas
constituents:
  STY:
    count: 200
densification:
  initial_density: 300.0  # kg/m3
  equilibration:
    - ensemble: min
    - ensemble: nvt
      temperature: 300
      ps: 10
    - ensemble: npt
      temperature: 300
      pressure: 10
      ps: 200
precure:
  preequilibration:
    ensemble: npt
    temperature: 300        # K
    pressure: 1             # bar
    ps: 200
  anneal:
    ncycles: 2
    initial_temperature: 300
    cycle_segments:
      - T: 300
        ps: 0
      - T: 600
        ps: 20
      - T: 600
        ps: 20
      - T: 300
        ps: 20
      - T: 300
        ps: 20
  postequilibration:
    ensemble: npt
    temperature: 300        # K
    pressure: 1             # bar
    ps: 100
CURE:
  controls:
    initial_search_radius: 0.5  # nm
    radial_increment: 0.25      # nm
    max_iterations: 150
    desired_conversion: 0.95
    late_threshhold: 0.85
  drag:
    trigger_distance: 0.6   # nm
    increment: 0.08         # nm
    limit: 0.3              # nm
    equilibration:
      - ensemble: min
      - ensemble: nvt
        temperature: 600
        nsteps: 1000
      - ensemble: npt
        temperature: 600
        pressure: 1
        nsteps: 2000
  relax:
    increment: 0.08         # nm
    equilibration:
      - ensemble: min
      - ensemble: nvt
        temperature: 600
        nsteps: 1000
      - ensemble: npt
        temperature: 600
        pressure: 1
        nsteps: 2000
  equilibrate:
    ensemble: npt
    temperature: 300       # K
    pressure: 1            # bar
    ps: 100
  gromacs:
    rdefault: 0.9          # nm
postcure:
  anneal:
    ncycles: 2
    initial_temperature: 300
    cycle_segments:
      - T: 300
        ps: 0
      - T: 600
        ps: 20
      - T: 600
        ps: 20
      - T: 300
        ps: 20
      - T: 300
        ps: 20
  postequilibration:
    ensemble: npt
    temperature: 300       # K
    pressure: 1            # bar
    ps: 100
reactions:
  - name:        sty1_1
    stage:       cure
    reactants:
      1: STY
      2: STY
    product:     STY~C1-C2~STY
    probability: 1.0
    atoms:
      A:
        reactant: 1
        resid: 1
        atom: C1
        z: 1
      B:
        reactant: 2
        resid: 1
        atom: C2
        z: 1
    bonds:
      - atoms: [A, B]
        order: 1
  - name:         styCC
    stage:        cap
    reactants:
      1: STY
    product:      STYCC
    probability:  1.0
    atoms:
      A:
        reactant: 1
        resid: 1
        atom: C1
        z: 1
      B:
        reactant: 1
        resid: 1
        atom: C2
        z: 1
    bonds:
      - atoms: [A, B]
        order: 2

A few things to note:

• charge_method: gas uses gas-phase AM1-BCC charges, which are faster than the default BCC charges and adequate for a tutorial run.

• The constituents block requests 200 styrene monomers — large enough to be interesting but small enough to finish in a few hours on a workstation.

• The CURE.gromacs.rdefault key sets the non-bonded cutoff radius for CURE-stage MD runs.

• All IMPORTANT DISCLAIMER caveats from the tutorial index apply: this is not a production build.