Workflow: md_launch.cwl

Fetched 2023-01-03 22:12:00 GMT
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Inputs

ID Type Title Doc
step1_pdb_files File[]
step5_genion_config String
step2_editconf_config String
step8_make_ndx_config String
step14_mdrun_md_config String
step13_grompp_md_config String
step6_grompp_min_config String
step9_grompp_nvt_config String
step11_grompp_npt_config String
step4_grompp_genion_config String

Steps

ID Runs Label Doc
launch_workflow
md_list.cwl (Workflow)
Molecular Dynamics Simulation.

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.

Outputs

ID Type Label Doc
top_dir Directory[] collected simulation output data

Collection of output directories returned by the md_list.cwl workflows.

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