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BioExcel AMBER ABC Setup - Drew-Dickerson Dodecamer DNA

W-18 · ABC MD Setup

v126 stages0 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. 01Create DNA system topology (leap)
    Consumes
    leap_gen_top_config, dna_pdb
    Produces
    leap_pdb, leap_top, leap_crd
  2. 02Create solvent box and solvate DNA system (leap)
    Consumes
    leap_solvate_config, leap_pdb
    Produces
    solv_pdb, solv_top, solv_crd
  3. 03Add ions at 100 mM concentration (leap)
    Consumes
    leap_add_ions_config, solv_pdb
    Produces
    ions_pdb, ions_top, ions_crd
  4. 04Randomize ion positions (cpptraj)
    Consumes
    cpptraj_randomize_ions_config, ions_top, ions_crd
    Produces
    rand_ions_crd, rand_ions_pdb
  5. 05Hydrogen mass repartitioning for 4 fs timestep (parmed)
    Consumes
    ions_top
    Produces
    top_4fs
  6. 06Equilibration step 1 - Minimization with restraints (sander)
    Consumes
    sander_eq1_config, top_4fs, step1_mdin, rand_ions_crd
    Produces
    eq1_traj, eq1_rst, eq1_log, eq1_mdinfo
  7. 07Extract eq1 minimization energy (process_minout)
    Consumes
    process_eq1_config, eq1_log
    Produces
    eq1_dat
  8. 08Equilibration step 2 - Heating with restraints (sander)
    Consumes
    sander_eq2_config, top_4fs, step2_mdin, eq1_rst
    Produces
    eq2_traj, eq2_rst, eq2_log, eq2_mdinfo
  9. 09Extract eq2 temperature (process_mdout)
    Consumes
    process_eq2_config, eq2_log
    Produces
    eq2_dat
  10. 10Equilibration step 3 - Minimization with restraints (sander)
    Consumes
    sander_eq3_config, top_4fs, step3_mdin, eq2_rst
    Produces
    eq3_traj, eq3_rst, eq3_log, eq3_mdinfo
  11. 11Extract eq3 minimization energy (process_minout)
    Consumes
    process_eq3_config, eq3_log
    Produces
    eq3_dat
  12. 12Equilibration step 4 - Minimization with restraints (sander)
    Consumes
    sander_eq4_config, top_4fs, step4_mdin, eq3_rst
    Produces
    eq4_traj, eq4_rst, eq4_log, eq4_mdinfo
  13. 13Extract eq4 minimization energy (process_minout)
    Consumes
    process_eq4_config, eq4_log
    Produces
    eq4_dat
  14. 14Equilibration step 5 - Minimization without restraints (sander)
    Consumes
    sander_eq5_config, top_4fs, step5_mdin, eq4_rst
    Produces
    eq5_traj, eq5_rst, eq5_log, eq5_mdinfo
  15. 15Extract eq5 minimization energy (process_minout)
    Consumes
    process_eq5_config, eq5_log
    Produces
    eq5_dat
  16. 16Equilibration step 6 - NPT with restraints (sander)
    Consumes
    sander_eq6_config, top_4fs, step6_mdin, eq5_rst
    Produces
    eq6_traj, eq6_rst, eq6_log, eq6_mdinfo
  17. 17Extract eq6 pressure and density (process_mdout)
    Consumes
    process_eq6_config, eq6_log
    Produces
    eq6_dat
  18. 18Equilibration step 7 - NPT with restraints (sander)
    Consumes
    sander_eq7_config, top_4fs, step7_mdin, eq6_rst
    Produces
    eq7_traj, eq7_rst, eq7_log, eq7_mdinfo
  19. 19Extract eq7 pressure and density (process_mdout)
    Consumes
    process_eq7_config, eq7_log
    Produces
    eq7_dat
  20. 20Equilibration step 8 - NPT with backbone restraints (sander)
    Consumes
    sander_eq8_config, top_4fs, step8_mdin, eq7_rst
    Produces
    eq8_traj, eq8_rst, eq8_log, eq8_mdinfo
  21. 21Extract eq8 pressure and density (process_mdout)
    Consumes
    process_eq8_config, eq8_log
    Produces
    eq8_dat
  22. 22Equilibration step 9 - NPT without restraints (sander)
    Consumes
    sander_eq9_config, top_4fs, step9_mdin, eq8_rst
    Produces
    eq9_traj, eq9_rst, eq9_log, eq9_mdinfo
  23. 23Extract eq9 pressure and density (process_mdout)
    Consumes
    process_eq9_config, eq9_log
    Produces
    eq9_dat
  24. 24Equilibration step 10 - NPT production equilibration (sander)
    Consumes
    sander_eq10_config, top_4fs, step10_mdin, eq9_rst
    Produces
    eq10_traj, eq10_rst, eq10_log, eq10_mdinfo
  25. 25Extract eq10 pressure and density (process_mdout)
    Consumes
    process_eq10_config, eq10_log
    Produces
    eq10_dat
  26. 26Free MD production simulation (sander)
    Consumes
    sander_md_config, top_4fs, md_mdin, eq10_rst
    Produces
    md_traj, md_rst, md_log, md_mdinfo

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