- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
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. |
https://w3id.org/cwl/view/git/97122f21048a5ac4a12b21059b751d1d07050cbd/md_launch.cwl