04 - Amber simulations

Prerequisite(s): 03-tleap

Minimization

TODO:

YAML

# Additional context for minimization
input_dir: "$SLURM_SUBMIT_DIR/inputs"
output_dir: "$SLURM_SUBMIT_DIR/outputs"
compute_platform: "mpi"

sbatch_options:
  nodes: 2
  ntasks-per-node: 48
  output: slurm-%j.out
  error: slurm-%j.err
  time: "1-00:00:00"
  cluster: mpi
  partition: mpi

01_min

YAML

  - stage_name: 01_min
    topo_path: "$SLURM_SUBMIT_DIR/inputs/mol.prmtop"
    prev_restart_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    ref_coord_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    input_kwargs:
      imin: 1
      ntx: 1
      irest: 0
      ntmin: 1
      maxcyc: 5000
      ncyc: 1000
      ntr: 1
      restraint_wt: 5.0
      restraintmask: "!(@H=)"
      ntb: 1
      ntf: 1
      ntc: 1
      cut: 10.0
      ntxo: 2
      ntwr: 200
      ntpr: 1
      ntwx: 200
      ioutfm: 1
      iwrap: 1

02_min

YAML

  - stage_name: 02_min
    topo_path: "$SLURM_SUBMIT_DIR/inputs/mol.prmtop"
    ref_coord_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    input_kwargs:
      imin: 1
      ntx: 1
      irest: 0
      ntmin: 1
      maxcyc: 5000
      ncyc: 1000
      ntr: 1
      restraint_wt: 5.0
      restraintmask: "!(:WAT) & !(@H=) & !(:Na+,Cl-)"
      ntb: 1
      ntf: 1
      ntc: 1
      cut: 10.0
      ntxo: 2
      ntwr: 200
      ntpr: 1
      ntwx: 200
      ioutfm: 1
      iwrap: 1

03_min

YAML

  - stage_name: 03_min
    topo_path: "$SLURM_SUBMIT_DIR/inputs/mol.prmtop"
    ref_coord_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    input_kwargs:
      imin: 1
      ntx: 1
      irest: 0
      ntmin: 1
      maxcyc: 5000
      ncyc: 1000
      ntr: 1
      restraint_wt: 2.0
      restraintmask: "!(:WAT) & (@C,CA,N,O,O5',P,O3',C3',C4',C5')"
      ntb: 1
      ntf: 1
      ntc: 1
      cut: 10.0
      ntxo: 2
      ntwr: 200
      ntpr: 1
      ntwx: 200
      ioutfm: 1
      iwrap: 1

04_min

YAML

  - stage_name: 04_min
    topo_path: "$SLURM_SUBMIT_DIR/inputs/mol.prmtop"
    ref_coord_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    input_kwargs:
      imin: 1
      ntx: 1
      irest: 0
      ntmin: 1
      maxcyc: 5000
      ncyc: 1000
      ntr: 1
      restraint_wt: 1.0
      restraintmask: "!(:WAT) & (@C,CA,N,O,O5',P,O3',C3',C4',C5')"
      ntb: 1
      ntf: 1
      ntc: 1
      cut: 10.0
      ntxo: 2
      ntwr: 200
      ntpr: 1
      ntwx: 200
      ioutfm: 1
      iwrap: 1

Relation

TODO:

YAML

input_dir: "$SLURM_SUBMIT_DIR/inputs"
output_dir: "$SLURM_SUBMIT_DIR/outputs"
compute_platform: "mpi"

sbatch_options:
  nodes: 3
  ntasks-per-node: 48
  output: slurm-%j.out
  error: slurm-%j.err
  time: "3-00:00:00"
  cluster: mpi
  partition: mpi
  account: jdurrant

05_relax_nvt_r

YAML

  - stage_name: 05_relax_nvt_r
    topo_path: "$SLURM_SUBMIT_DIR/inputs/mol.prmtop"
    prev_restart_path: "$SLURM_SUBMIT_DIR/../../03-min/outputs/04_min.rst"
    ref_coord_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    input_kwargs:
      irest: 0
      ntx: 1
      ig: -1
      dt: 0.002
      nstlim: 10000
      nscm: 500
      ntr: 1
      restraint_wt: 1.0
      restraintmask: "!(:WAT) & (@C,CA,N,O,O5',P,O3',C3',C4',C5')"
      ntb: 1
      ntf: 2
      ntc: 2
      cut: 10.0
      ntt: 3
      tempi: 100.0
      temp0: 300.0
      gamma_ln: 5.0
      ntp: 0
      ntxo: 2
      ntwr: 500
      ntpr: 500
      ntwx: 500
      ioutfm: 1
      iwrap: 1

06_relax_npt_r

YAML

  - stage_name: 06_relax_npt_r
    topo_path: "$SLURM_SUBMIT_DIR/inputs/mol.prmtop"
    ref_coord_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    input_kwargs:
      irest: 1
      ntx: 5
      ig: -1
      dt: 0.002
      nstlim: 500000
      nscm: 500
      ntr: 1
      restraint_wt: 0.5
      restraintmask: "!(:WAT) & (@C,CA,N,O,O5',P,O3',C3',C4',C5')"
      ntb: 2
      ntf: 2
      ntc: 2
      cut: 10.0
      ntt: 3
      temp0: 300.0
      gamma_ln: 5.0
      ntp: 1
      barostat: 2
      pres0: 1.01325
      mcbarint: 100
      comp: 44.6
      taup: 1.0
      ntxo: 2
      ntwr: 5000
      ntpr: 500
      ntwx: 5000
      ioutfm: 1
      iwrap: 1

07_relax_npt

YAML

  - stage_name: 07_relax_npt
    topo_path: "$SLURM_SUBMIT_DIR/inputs/mol.prmtop"
    ref_coord_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    input_kwargs:
      irest: 1
      ntx: 5
      ig: -1
      dt: 0.002
      nstlim: 500000
      nscm: 500
      ntr: 0
      ntb: 2
      ntf: 2
      ntc: 2
      cut: 10.0
      ntt: 3
      temp0: 300.0
      gamma_ln: 5.0
      ntp: 1
      barostat: 2
      pres0: 1.01325
      mcbarint: 100
      comp: 44.6
      taup: 1.0
      ntxo: 2
      ntwr: 5000
      ntpr: 500
      ntwx: 5000
      ioutfm: 1
      iwrap: 1

Production

YAML

input_dir: "$SLURM_SUBMIT_DIR/inputs"
output_dir: "$SLURM_SUBMIT_DIR/outputs"
compute_platform: "cuda"

sbatch_options:
  nodes: 1
  ntasks-per-node: 2
  output: slurm-%j.out
  error: slurm-%j.err
  time: "6-00:00:00"
  cluster: gpu
  partition: a100
  gres: gpu:1
  account: jdurrant

08_prod_npt

The simulation employs the NPT ensemble with a time step of 0.002 ps (2.0 fs) for 50 million MD steps for a total of 100 ns. Temperature control is achieved through Langevin dynamics with a target temperature of 300 K and a collision frequency of 5.0 ps^-1. Pressure control is implemented using the isotropic position scaling method with a Berendsen barostat, targeting a pressure of 1.01325 bar and a pressure relaxation time of 1.0 ps. Periodic boundary conditions are used for non-bonded interactions with a 10.0 Å cutoff. Covalent bonds involving hydrogen are constrained with the SHAKE algorithm. Coordinates are written every 5000 steps (10 ps) and energy information every 500 steps (1 ps).

YAML

  - stage_name: 08_prod_npt
    topo_path: "$SLURM_SUBMIT_DIR/inputs/mol.prmtop"
    prev_restart_path: "$SLURM_SUBMIT_DIR/../../04-relax/{{ RUN_NAME }}/outputs/07_relax_npt.rst"
    ref_coord_path: "$SLURM_SUBMIT_DIR/inputs/mol.inpcrd"
    input_kwargs:
      irest: 1
      ntx: 5
      ig: -1
      dt: 0.002
      nstlim: 50000000
      nscm: 500
      ntr: 0
      ntb: 2
      ntf: 2
      ntc: 2
      cut: 10.0
      ntt: 3
      temp0: 300.0
      gamma_ln: 5.0
      ntp: 1
      barostat: 2
      pres0: 1.01325
      mcbarint: 100
      comp: 44.6
      taup: 1.0
      ntxo: 2
      ntwr: 5000
      ntpr: 500
      ntwx: 5000
      ioutfm: 1
      iwrap: 1