global_properties:
  working_dir_path: biobb_wf_protein-complex_md_setup
  can_write_console_log: False
  run_md: false

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

step2_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/step2_extract_molecule/output_molecule_path
    input_structure2: /data/ions.pdb
    output_structure_path: protein.ions.pdb

step4_fix_side_chain:
  tool: fix_side_chain
  paths:
    input_pdb_path: dependency/step00_cat_pdb/output_structure_path
    output_pdb_path: fixsidechain.pdb

step5_pdb2gmx:
  tool: pdb2gmx
  paths:
    input_pdb_path:  dependency/step4_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

step9_make_ndx:
  tool: make_ndx
  paths:
    input_structure_path: /data/ligand.gro
    output_ndx_path: ligand.index.ndx
  properties:
    selection: 0 & ! a H*

step10_genrestr:
  tool: genrestr
  paths:
    input_structure_path: /data/ligand.gro
    input_ndx_path: dependency/step9_make_ndx/output_ndx_path
    output_itp_path: ligand.posres.itp
  properties:
    force_constants: 1000 1000 1000
    restrained_group: System

step11_gmx_trjconv_str_protein:
  tool: gmx_trjconv_str
  paths:
    input_structure_path: dependency/step5_pdb2gmx/output_gro_path
    input_top_path: dependency/step5_pdb2gmx/output_gro_path
    output_str_path: protein_H.pdb
  properties:
    selection: System

step12_gmx_trjconv_str_ligand:
  tool: gmx_trjconv_str
  paths:
    input_structure_path: /data/ligand.gro
    input_top_path: /data/ligand.gro
    output_str_path: ligand_H.pdb
  properties:
    selection: System

step13_cat_pdb_hydrogens:
  tool: cat_pdb
  paths:
    input_structure1: dependency/step11_gmx_trjconv_str_protein/output_str_path
    input_structure2: dependency/step12_gmx_trjconv_str_ligand/output_str_path
    output_structure_path: complex_H.pdb

step14_append_ligand:
  tool: append_ligand
  paths:
    input_top_zip_path: dependency/step5_pdb2gmx/output_top_zip_path
    input_posres_itp_path: dependency/step10_genrestr/output_itp_path
    input_itp_path: /data/ligand.itp
    output_top_zip_path: complex.top.zip
  properties:
    posres_name: POSRES_LIGAND

step15_editconf:
  tool: editconf
  paths:
    input_gro_path: dependency/step13_cat_pdb_hydrogens/output_structure_path
    output_gro_path: complex.editconf.pdb
  properties:
    distance_to_molecule: 0.8
    box_type: octahedron

step16_solvate:
  tool: solvate
  paths:
    input_solute_gro_path: dependency/step15_editconf/output_gro_path
    output_gro_path: solvate.gro
    input_top_zip_path: dependency/step14_append_ligand/output_top_zip_path
    output_top_zip_path: solvate_top.zip

step17_grompp_genion:
  tool: grompp
  paths:
    input_gro_path: dependency/step16_solvate/output_gro_path
    input_top_zip_path: dependency/step16_solvate/output_top_zip_path
    output_tpr_path: complex.gppion.tpr
  properties:
    simulation_type: minimization
    maxwarn: 1
    mdp:
      nsteps: 5000

step18_genion:
  tool: genion
  paths:
    input_tpr_path: dependency/step17_grompp_genion/output_tpr_path
    output_gro_path: genion.gro
    input_top_zip_path: dependency/step16_solvate/output_top_zip_path
    output_top_zip_path: genion_top.zip
  properties:
    neutral: True
    concentration: 0.05

step19_grompp_min:
  tool: grompp
  paths:
    input_gro_path: dependency/step18_genion/output_gro_path
    input_top_zip_path: dependency/step18_genion/output_top_zip_path
    output_tpr_path: gppmin.tpr
  properties:
    mdp:
      nsteps: 5000
      emtol: 500
      emstep: 0.01
    simulation_type: minimization

step20_mdrun_min:
  tool: mdrun
  paths:
    input_tpr_path: dependency/step19_grompp_min/output_tpr_path
    output_trr_path: complex.min.trr
    output_gro_path: complex.min.gro
    output_edr_path: complex.min.edr
    output_log_path: complex.min.log

step21_gmx_energy_min:
  tool: gmx_energy
  paths:
    input_energy_path: dependency/step20_mdrun_min/output_edr_path
    output_xvg_path: complex.min.energy.xvg
  properties:
    terms: [Potential]

step22_make_ndx:
  tool: make_ndx
  paths:
    input_structure_path: dependency/step20_mdrun_min/output_gro_path
    output_ndx_path: complex.index.ndx
  properties:
    selection: "\"Protein\"|\"Other\"" 

step23_grompp_nvt:
  tool: grompp
  paths:
    input_gro_path: dependency/step20_mdrun_min/output_gro_path
    input_top_zip_path: dependency/step18_genion/output_top_zip_path
    input_ndx_path: dependency/step22_make_ndx/output_ndx_path
    output_tpr_path: complex.gppnvt.tpr
  properties:
    mdp:
      nsteps: 50000
      tc-grps: "Protein_Other Water_and_ions"
      Define: -DPOSRES -DPOSRES_LIGAND
    simulation_type: nvt

step24_mdrun_nvt:
  tool: mdrun
  paths:
    input_tpr_path: dependency/step23_grompp_nvt/output_tpr_path
    output_trr_path: complex.nvt.trr
    output_gro_path: complex.nvt.gro
    output_edr_path: complex.nvt.edr
    output_log_path: complex.nvt.log
    output_cpt_path: complex.nvt.cpt

step25_gmx_energy_nvt:
  tool: gmx_energy
  paths:
    input_energy_path: dependency/step24_mdrun_nvt/output_edr_path
    output_xvg_path: complex.nvt.temp.xvg
  properties:
    terms: [Temperature]

step26_grompp_npt:
  tool: grompp
  paths:
    input_gro_path: dependency/step24_mdrun_nvt/output_gro_path
    input_top_zip_path: dependency/step18_genion/output_top_zip_path
    input_ndx_path: dependency/step22_make_ndx/output_ndx_path
    output_tpr_path: complex.gppnpt.tpr
    input_cpt_path: dependency/step24_mdrun_nvt/output_cpt_path
  properties:
    mdp:
      nsteps: 50000
      type: npt
      tc-grps: "Protein_Other Water_and_ions"
      Define: -DPOSRES -DPOSRES_LIGAND
    simulation_type: npt

step27_mdrun_npt:
  tool: mdrun
  paths:
    input_tpr_path: dependency/step26_grompp_npt/output_tpr_path
    output_trr_path: complex.npt.trr
    output_gro_path: complex.npt.gro
    output_edr_path: complex.npt.edr
    output_log_path: complex.npt.log
    output_cpt_path: complex.npt.cpt

step28_gmx_energy_npt:
  tool: gmx_energy
  paths:
    input_energy_path: dependency/step27_mdrun_npt/output_edr_path
    output_xvg_path: complex.npt.PD.xvg
  properties:
    terms: [Pressure,Density]

step29_grompp_md:
  tool: grompp
  paths:
    input_gro_path: dependency/step27_mdrun_npt/output_gro_path
    input_ndx_path: dependency/step22_make_ndx/output_ndx_path
    input_top_zip_path: dependency/step18_genion/output_top_zip_path
    output_tpr_path: complex.gppmd.tpr
    input_cpt_path: dependency/step27_mdrun_npt/output_cpt_path
  properties:
    mdp:
      nsteps: 250000
      tc-grps: "Protein_Other Water_and_ions"
    simulation_type: free

step30_mdrun_md:
  tool: mdrun
  paths:
    input_tpr_path: dependency/step29_grompp_md/output_tpr_path
    output_trr_path: complex.md.trr
    output_gro_path: complex.md.gro
    output_edr_path: complex.md.edr
    output_log_path: complex.md.log
    output_cpt_path: complex.md.cpt

step34_gmx_image:
  tool: gmx_image
  paths:
    input_traj_path: dependency/step30_mdrun_md/output_trr_path
    input_top_path: dependency/step19_grompp_min/output_tpr_path
    input_index_path: dependency/step22_make_ndx/output_ndx_path
    output_traj_path: complex.imaged.trr
  properties:
    center_selection: "Protein_Other"
    output_selection: System
    pbc: "mol"
    center: True

step34b_gmx_image2:
  tool: gmx_image
  paths:
    input_traj_path: dependency/step34_gmx_image/output_traj_path
    input_top_path: dependency/step19_grompp_min/output_tpr_path
    input_index_path: dependency/step22_make_ndx/output_ndx_path
    output_traj_path: complex.imaged.rot.xtc
  properties:
    fit_selection: "Protein_Other"
    output_selection: System
    fit: rot+trans

step35_gmx_trjconv_str:
  tool: gmx_trjconv_str
  paths:
    input_structure_path: dependency/step30_mdrun_md/output_gro_path
    input_top_path: dependency/step19_grompp_min/output_tpr_path
    input_index_path: dependency/step22_make_ndx/output_ndx_path
    output_str_path: complex.md.gro
  properties:
    pbc: "mol"
    selection: System

step31_rmsd_first:
  tool: gmx_rms
  paths:
    input_structure_path: dependency/step29_grompp_md/output_tpr_path
    input_traj_path: dependency/step34b_gmx_image2/output_traj_path
    input_index_path: dependency/step22_make_ndx/output_ndx_path
    output_xvg_path: complex.rmsd_first.xvg
  properties:
    selection: "Protein_Other"

step32_rmsd_exp:
  tool: gmx_rms
  paths:
    input_structure_path: dependency/step19_grompp_min/output_tpr_path
    input_traj_path: dependency/step34b_gmx_image2/output_traj_path
    input_index_path: dependency/step22_make_ndx/output_ndx_path
    output_xvg_path: complex.rmsd_exp.xvg
  properties:
    selection: "Protein_Other"

step33_gmx_rgyr:
  tool: gmx_rgyr
  paths:
    input_structure_path: dependency/step29_grompp_md/output_tpr_path
    input_traj_path: dependency/step34b_gmx_image2/output_traj_path
    input_index_path: dependency/step22_make_ndx/output_ndx_path
    output_xvg_path: complex.rgyr.xvg
  properties:
    selection: "Protein_Other"

# production MD
step36_grompp_md:
  tool: grompp
  paths:
    input_gro_path: dependency/step30_mdrun_md/output_gro_path
    input_top_zip_path: dependency/step18_genion/output_top_zip_path
    output_tpr_path: gppmdsim.tpr
    input_cpt_path: dependency/step30_mdrun_md/output_cpt_path
  properties:
    mdp:
      nsteps: 5000000
      dt: 0.002
      ref-t: 300 300
      nstxout: 100000
      nstxout-compressed: 500
    simulation_type: free