global_properties:
  working_dir_path: biobb_wf_md_setup
  can_write_console_log: False
  run_md: true

step0_reduce_remove_hydrogens:
  tool: reduce_remove_hydrogens
  paths:
    input_path: /data/structure.pdb
    output_path: structure.noH.pdb

step1_extract_molecule:
  tool: extract_molecule
  paths:
    input_structure_path: dependency/step0_reduce_remove_hydrogens/output_path
    output_molecule_path: protein.pdb

step00_cat_pdb:
  tool: cat_pdb
  paths:
    input_structure1: dependency/step1_extract_molecule/output_molecule_path
    input_structure2: /data/ions.pdb
    output_structure_path: protein.ions.pdb

step2_fix_side_chain:
  tool: fix_side_chain
  paths:
    input_pdb_path: dependency/step00_cat_pdb/output_structure_path
    output_pdb_path: fixsidechain.pdb

step4_pdb2gmx:
  tool: pdb2gmx
  paths:
    input_pdb_path: dependency/step2_fix_side_chain/output_pdb_path
    output_gro_path: pdb2gmx.gro
    output_top_zip_path: pdb2gmx_top.zip
  properties:
    force_field: amber99sb
    water_type: tip3p

step5_editconf:
  tool: editconf
  paths:
    input_gro_path: dependency/step4_pdb2gmx/output_gro_path
    output_gro_path: editconf.pdb
  properties:
    distance_to_molecule: 0.8
    box_type: octahedron

step6_solvate:
  tool: solvate
  paths:
    input_solute_gro_path: dependency/step5_editconf/output_gro_path
    output_gro_path: solvate.gro
    input_top_zip_path: dependency/step4_pdb2gmx/output_top_zip_path
    output_top_zip_path: solvate_top.zip

step7_grompp_genion:
  tool: grompp
  paths:
    input_gro_path: dependency/step6_solvate/output_gro_path
    input_top_zip_path: dependency/step6_solvate/output_top_zip_path
    output_tpr_path: gppion.tpr
  properties:
    simulation_type: minimization
    maxwarn: 1
    mdp:
      nsteps: 5000

step8_genion:
  tool: genion
  paths:
    input_tpr_path: dependency/step7_grompp_genion/output_tpr_path
    output_gro_path: genion.gro
    input_top_zip_path: dependency/step6_solvate/output_top_zip_path
    output_top_zip_path: genion_top.zip
  properties:
    neutral: True
    concentration: 0.05

step9_grompp_min:
  tool: grompp
  paths:
    input_gro_path: dependency/step8_genion/output_gro_path
    input_top_zip_path: dependency/step8_genion/output_top_zip_path
    output_tpr_path: gppmin.tpr
  properties:
    mdp:
      nsteps: 5000
      emtol: 500
    simulation_type: minimization

step10_mdrun_min:
  tool: mdrun
  paths:
    input_tpr_path: dependency/step9_grompp_min/output_tpr_path
    output_trr_path: min.trr
    output_gro_path: min.gro
    output_edr_path: min.edr
    output_log_path: min.log

step100_make_ndx:
  tool: make_ndx
  paths:
    input_structure_path: dependency/step10_mdrun_min/output_gro_path
    output_ndx_path: str_index.ndx
  properties:
    selection: "System"

step11_grompp_nvt:
  tool: grompp
  paths:
    input_gro_path: dependency/step10_mdrun_min/output_gro_path
    input_ndx_path: dependency/step100_make_ndx/output_ndx_path
    input_top_zip_path: dependency/step8_genion/output_top_zip_path
    output_tpr_path: gppnvt.tpr
  properties:
    mdp:
      nsteps: 50000
      dt: 0.002
      Define: -DPOSRES
      tc-grps: "Protein Water_and_ions"
    simulation_type: nvt

step12_mdrun_nvt:
  tool: mdrun
  paths:
    input_tpr_path: dependency/step11_grompp_nvt/output_tpr_path
    output_trr_path: nvt.trr
    output_gro_path: nvt.gro
    output_edr_path: nvt.edr
    output_log_path: nvt.log
    output_cpt_path: nvt.cpt

step13_grompp_npt:
  tool: grompp
  paths:
    input_gro_path: dependency/step12_mdrun_nvt/output_gro_path
    input_ndx_path: dependency/step100_make_ndx/output_ndx_path
    input_top_zip_path: dependency/step8_genion/output_top_zip_path
    output_tpr_path: gppnpt.tpr
    input_cpt_path: dependency/step12_mdrun_nvt/output_cpt_path
  properties:
    mdp:
      nsteps: 50000
      tc-grps: "Protein Water_and_ions"
    simulation_type: npt

step14_mdrun_npt:
  tool: mdrun
  paths:
    input_tpr_path: dependency/step13_grompp_npt/output_tpr_path
    output_trr_path: npt.trr
    output_gro_path: npt.gro
    output_edr_path: npt.edr
    output_log_path: npt.log
    output_cpt_path: npt.cpt

step15_grompp_md:
  tool: grompp
  paths:
    input_gro_path: dependency/step14_mdrun_npt/output_gro_path
    input_ndx_path: dependency/step100_make_ndx/output_ndx_path
    input_top_zip_path: dependency/step8_genion/output_top_zip_path
    output_tpr_path: gppmd.tpr
    input_cpt_path: dependency/step14_mdrun_npt/output_cpt_path
  properties:
    mdp:
      nsteps: 250000
      tc-grps: "Protein Water_and_ions"
    simulation_type: free

step16_mdrun_md:
  tool: mdrun
  paths:
    input_tpr_path: dependency/step15_grompp_md/output_tpr_path
    output_trr_path: md.trr
    output_gro_path: md.gro
    output_edr_path: md.edr
    output_log_path: md.log
    output_cpt_path: md.cpt

step17_gmx_image1:
  tool: gmx_image
  paths:
    input_traj_path: dependency/step16_mdrun_md/output_trr_path
    input_top_path: dependency/step9_grompp_min/output_tpr_path
    input_index_path: dependency/step100_make_ndx/output_ndx_path
    output_traj_path: md.imaged.trr
  properties:
    center_selection: "Protein"
    output_selection: System
    pbc: "mol"
    center: true
    ur: compact

step18_gmx_image2:
  tool: gmx_image
  paths:
    input_traj_path: dependency/step17_gmx_image1/output_traj_path
    input_top_path: dependency/step9_grompp_min/output_tpr_path
    input_index_path: dependency/step100_make_ndx/output_ndx_path
    output_traj_path: md.imaged.rot.xtc
  properties:
    fit_selection: "Protein"
    output_selection: System  
    fit: rot+trans

step19_gmx_trjconv_str:
  tool: gmx_trjconv_str
  paths:
    input_structure_path: dependency/step16_mdrun_md/output_gro_path
    input_top_path: dependency/step9_grompp_min/output_tpr_path
    input_index_path: dependency/step100_make_ndx/output_ndx_path
    output_str_path: setup.top.pdb
  properties:
    pbc: "mol"
    selection: System

step20_gmx_energy:
  tool: gmx_energy
  paths:
    input_energy_path: dependency/step16_mdrun_md/output_edr_path
    output_xvg_path: setup.energy.xvg
  properties:
    xvg: xmgr
    terms: [Potential,Total-Energy]

step21_gmx_rgyr:
  tool: gmx_rgyr
  paths:
    input_structure_path: dependency/step15_grompp_md/output_tpr_path
    input_traj_path: dependency/step18_gmx_image2/output_traj_path
    input_index_path: dependency/step100_make_ndx/output_ndx_path
    output_xvg_path: setup.rgyr.xvg
  properties:
    xvg: xmgr
    selection: "Protein-H"

step22_rmsd_first:
  tool: gmx_rms
  paths:
    input_structure_path: dependency/step15_grompp_md/output_tpr_path
    input_traj_path: dependency/step18_gmx_image2/output_traj_path
    input_index_path: dependency/step100_make_ndx/output_ndx_path
    output_xvg_path: setup.rmsd_first.xvg
  properties:
    selection: "Protein-H"

step23_rmsd_exp:
  tool: gmx_rms
  paths:
    input_structure_path: dependency/step9_grompp_min/output_tpr_path
    input_traj_path: dependency/step18_gmx_image2/output_traj_path
    input_index_path: dependency/step100_make_ndx/output_ndx_path
    output_xvg_path: setup.rmsd_exp.xvg
  properties:
    selection: "Protein-H"

# production MD
step24_grompp_md:
  tool: grompp
  paths:
    input_gro_path: dependency/step16_mdrun_md/output_gro_path
    input_top_zip_path: dependency/step8_genion/output_top_zip_path
    output_tpr_path: gppmdsim.tpr
    input_cpt_path: dependency/step16_mdrun_md/output_cpt_path
  properties:
    mdp:
      nsteps: 5000000
      dt: 0.002
      ref-t: 300 300
      nstxout: 100000
      nstxout-compressed: 500
    simulation_type: free