CWL Workflow: Molecular Dynamics Simulation.

Workflow: Molecular Dynamics Simulation.

Fetched 2023-01-10 18:00:46 GMT

Verified with cwltool version 3.1.20221201130942

CWL version of the md_list.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 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/Outputs

This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
step1_pdb_file	File	Input file	Molecule to process (PDB format)
step5_genion_config	String	Genion configuration dictionary
step2_editconf_config	String	Editconf configuration dictionary
step8_make_ndx_config	String	GROMACS make_ndx configuration dictionary
step14_mdrun_md_config	String	GROMACS mdrun configuration dictionary
step13_grompp_md_config	String	GROMACS grompp configuration dictionary
step6_grompp_min_config	String	GROMACS grompp configuration dictionary
step9_grompp_nvt_config	String	GROMACS grompp configuration dictionary
step11_grompp_npt_config	String	GROMACS grompp configuration dictionary
step4_grompp_genion_config	String	GROMACS grompp configuration dictionary

Steps

ID	Runs	Label	Doc
step5_genion	biobb/biobb_adapters/cwl/biobb_md/gromacs/genion.cwl (CommandLineTool)
step1_pdb2gmx	biobb/biobb_adapters/cwl/biobb_md/gromacs/pdb2gmx.cwl (CommandLineTool)
step3_solvate	biobb/biobb_adapters/cwl/biobb_md/gromacs/solvate.cwl (CommandLineTool)
step2_editconf	biobb/biobb_adapters/cwl/biobb_md/gromacs/editconf.cwl (CommandLineTool)
step8_make_ndx	biobb/biobb_adapters/cwl/biobb_md/gromacs/make_ndx.cwl (CommandLineTool)
step14_mdrun_md	biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl (CommandLineTool)
step7_mdrun_min	biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl (CommandLineTool)
step10_mdrun_nvt	biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl (CommandLineTool)
step12_mdrun_npt	biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl (CommandLineTool)
step13_grompp_md	biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl (CommandLineTool)	Wrapper of the GROMACS grompp module	The GROMACS preprocessor module needs to be feeded with the input system and the dynamics parameters to create a portable binary run input file TPR. The dynamics parameters are specified in the mdp section of the configuration YAML file. The parameter names and defaults are the same as the ones in the official MDP specification.
step6_grompp_min	biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl (CommandLineTool)	Wrapper of the GROMACS grompp module	The GROMACS preprocessor module needs to be feeded with the input system and the dynamics parameters to create a portable binary run input file TPR. The dynamics parameters are specified in the mdp section of the configuration YAML file. The parameter names and defaults are the same as the ones in the official MDP specification.
step9_grompp_nvt	biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl (CommandLineTool)	Wrapper of the GROMACS grompp module	The GROMACS preprocessor module needs to be feeded with the input system and the dynamics parameters to create a portable binary run input file TPR. The dynamics parameters are specified in the mdp section of the configuration YAML file. The parameter names and defaults are the same as the ones in the official MDP specification.
step11_grompp_npt	biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl (CommandLineTool)	Wrapper of the GROMACS grompp module	The GROMACS preprocessor module needs to be feeded with the input system and the dynamics parameters to create a portable binary run input file TPR. The dynamics parameters are specified in the mdp section of the configuration YAML file. The parameter names and defaults are the same as the ones in the official MDP specification.
step4_grompp_genion	biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl (CommandLineTool)	Wrapper of the GROMACS grompp module	The GROMACS preprocessor module needs to be feeded with the input system and the dynamics parameters to create a portable binary run input file TPR. The dynamics parameters are specified in the mdp section of the configuration YAML file. The parameter names and defaults are the same as the ones in the official MDP specification.
step15_gather_outputs	md_gather.cwl (ExpressionTool)		This javascript takes three inputs: a list of files; a project file; and an optional string. It will create a directory named after the project file and optional string, populate that directory with the files in the list, and return the directory.

Outputs

ID	Type	Label	Doc
dir	Directory	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.

Permalink: https://w3id.org/cwl/view/git/97122f21048a5ac4a12b21059b751d1d07050cbd/md_list.cwl