CWL version of the md_list.py workflow for HPC. This performs a system setup and runs a molecular dynamics simulation on the structure passed to this workflow. This workflow uses the md_gather.cwl sub-workflow to gather the outputs together to return these. To work with more than one structure this workflow can be called from either the md_launch.cwl workflow, or the md_launch_mutate.cwl workflow. These use scatter for parallelising the workflow. md_launch.cwl operates on a list of individual input molecule files. md_launch_mutate.cwl operates on a single input molecule file, and a list of mutations to apply to that molecule. Within that list of mutations, a value of 'WT' will indicate that the molecule should be simulated without any mutation being applied.
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Inputs
ID | Name | Description | Type |
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step1_pdb_file | Input file | Molecule to process (PDB format) |
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step2_editconf_config | Editconf configuration dictionary | n/a |
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step4_grompp_genion_config | GROMACS grompp configuration dictionary | n/a |
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step5_genion_config | Genion configuration dictionary | n/a |
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step6_grompp_min_config | GROMACS grompp configuration dictionary | n/a |
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step8_make_ndx_config | GROMACS make_ndx configuration dictionary | n/a |
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step9_grompp_nvt_config | GROMACS grompp configuration dictionary | n/a |
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step11_grompp_npt_config | GROMACS grompp configuration dictionary | n/a |
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step13_grompp_md_config | GROMACS grompp configuration dictionary | n/a |
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step14_mdrun_md_config | GROMACS mdrun configuration dictionary | n/a |
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Steps
ID | Name | Description |
---|---|---|
step1_pdb2gmx | Create Protein System Topology | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.pdb2gmx |
step2_editconf | Create Solvent Box | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.editconf |
step3_solvate | Fill the Box with Water Molecules | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.solvate |
step4_grompp_genion | Add Ions - part 1 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp |
step5_genion | Add Ions - part 2 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.genion |
step6_grompp_min | Energetically Minimize the System - part 1 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp |
step7_mdrun_min | Energetically Minimize the System - part 2 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun |
step8_make_ndx | Generate GROMACS index file | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.make_ndx |
step9_grompp_nvt | Equilibrate the System (NVT) - part 1 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp |
step10_mdrun_nvt | Equilibrate the System (NVT) - part 2 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun |
step11_grompp_npt | Equilibrate the System (NPT) - part 1 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp |
step12_mdrun_npt | Equilibrate the System (NPT) - part 2 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun |
step13_grompp_md | Free Molecular Dynamics Simulation - part 1 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp |
step14_mdrun_md | Free Molecular Dynamics Simulation - part 2 | https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.mdrun |
step15_gather_outputs | Archiving outputs to be returned to user | This uses the local md_gather.cwl workflow to gather all desired output files. A filter for missing files is applied (pickValue: all_non_null), which requires using a runner which is compliant with v1.2.0, or later, CWL standards. |
Outputs
ID | Name | Description | Type |
---|---|---|---|
dir | whole workflow output | outputs from the whole workflow, containing these optional files: step14_mdrun_md/output_trr_file: Raw trajectory from the free simulation step step14_mdrun_md/output_gro_file: Raw structure from the free simulation step. step14_mdrun_md/output_cpt_file: GROMACS portable checkpoint file, allowing to restore (continue) the simulation from the last step of the setup process. step13_grompp_md/output_tpr_file: GROMACS portable binary run input file, containing the starting structure of the simulation, the molecular topology and all the simulation parameters. step5_genion/output_top_zip_file: GROMACS topology file, containing the molecular topology in an ASCII readable format. |
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Version History
Version 1 (earliest) Created 20th May 2021 at 15:41 by Douglas Lowe
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Views: 2163 Downloads: 215
Created: 20th May 2021 at 15:41
Last updated: 20th May 2021 at 15:48
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