Molecular Dynamics Simulation
Version 1

Work-in-progress

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.

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
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Created: 20th May 2021 at 15:41

Last updated: 20th May 2021 at 15:48

Last used: 23rd Jun 2021 at 12:23

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Version 1 Created 20th May 2021 at 15:41 by Douglas Lowe

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