Molecular Dynamics Simulation.
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

CWL version of the mdlist.cwl 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 mdgather.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 mdlaunch.cwl workflow, or the mdlaunchmutate.cwl workflow. These use scatter for parallelising the workflow. mdlaunch.cwl operates on a list of individual input molecule files. mdlaunchmutate.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.

Inputs

ID Name Description Type
step1_pdb_file Input file Molecule to process (PDB format)
  • File
step2_editconf_config Editconf configuration dictionary n/a
  • string
step4_grompp_genion_config GROMACS grompp configuration dictionary n/a
  • string
step5_genion_config Genion configuration dictionary n/a
  • string
step6_grompp_min_config GROMACS grompp configuration dictionary n/a
  • string
step8_make_ndx_config GROMACS make_ndx configuration dictionary n/a
  • string
step9_grompp_nvt_config GROMACS grompp configuration dictionary n/a
  • string
step11_grompp_npt_config GROMACS grompp configuration dictionary n/a
  • string
step13_grompp_md_config GROMACS grompp configuration dictionary n/a
  • string
step14_mdrun_md_config GROMACS mdrun configuration dictionary n/a
  • string

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.
  • Directory
Total size: 648 KB
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Views: 238

Created: 22nd Jun 2021 at 09:55

Last updated: 23rd Aug 2021 at 20:22

Last used: 19th Sep 2021 at 08:39

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main @ 97122f2 (earliest) Created 22nd Jun 2021 at 09:55 by Douglas Lowe

Improving documentation of workflows.


Locked main 97122f2

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