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BioExcel MD Setup - Lysozyme 1AKI

W-03 · GROMACS MD Setup

v117 stages1 clones0

The pipeline

Every stage picks its own compute target. Temple Compute OS resolves the dependencies between them and moves the data across each boundary.

  1. 01Download 1AKI structure from PDB
    Consumes
    fetch_pdb_config, src_conda_env_yaml
    Produces
    downloaded_pdb
  2. 02Model missing side-chain atoms
    Consumes
    downloaded_pdb, src_conda_env_yaml
    Produces
    fixed_pdb
  3. 03Build GROMACS topology (pdb2gmx)
    Consumes
    fixed_pdb, src_conda_env_yaml
    Produces
    system_gro, pdb2gmx_top
  4. 04Define cubic simulation box
    Consumes
    editconf_config, system_gro, src_conda_env_yaml
    Produces
    boxed_gro
  5. 05Fill box with SPC water molecules
    Consumes
    boxed_gro, pdb2gmx_top, src_conda_env_yaml
    Produces
    solvated_gro, solvated_top
  6. 06Compile ion run file (grompp)
    Consumes
    grompp_ions_config, solvated_gro, solvated_top, src_conda_env_yaml
    Produces
    ions_tpr
  7. 07Add neutralizing ions
    Consumes
    genion_config, ions_tpr, solvated_top, src_conda_env_yaml
    Produces
    ionized_gro, ionized_top
  8. 08Compile minimization run file (grompp)
    Consumes
    grompp_minimize_config, ionized_gro, ionized_top, src_conda_env_yaml
    Produces
    min_tpr
  9. 09Energy minimization (steepest descent)
    Consumes
    min_tpr, src_conda_env_yaml
    Produces
    minimized_gro
  10. 10Compile NVT run file (grompp)
    Consumes
    grompp_nvt_config, minimized_gro, ionized_top, src_conda_env_yaml
    Produces
    nvt_tpr
  11. 11NVT equilibration (10 ps, restrained)
    Consumes
    nvt_tpr, src_conda_env_yaml
    Produces
    nvt_gro, nvt_cpt
  12. 12Compile NPT run file (grompp)
    Consumes
    grompp_npt_config, nvt_gro, nvt_cpt, ionized_top, src_conda_env_yaml
    Produces
    npt_tpr
  13. 13NPT equilibration (10 ps, restrained)
    Consumes
    npt_tpr, src_conda_env_yaml
    Produces
    npt_gro, npt_cpt
  14. 14Compile free MD run file (grompp)
    Consumes
    grompp_free_config, npt_gro, npt_cpt, ionized_top, src_conda_env_yaml
    Produces
    md_tpr
  15. 15Free MD simulation (100 ps)
    Consumes
    md_tpr, src_conda_env_yaml
    Produces
    md_gro, md_trr
  16. 16Center protein and fix PBC in trajectory
    Consumes
    center_config, md_trr, md_tpr, src_conda_env_yaml
    Produces
    imaged_trr
  17. 17Extract dry protein structure from trajectory
    Consumes
    dry_trjconv_config, md_gro, md_tpr, src_conda_env_yaml
    Produces
    dry_gro

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