Example of setting up a simulation system
Version 2

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Workflow Type: Common Workflow Language
Work-in-progress

CWL version of the md_list.cwl workflow for HPC.

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SEEK ID: https://workflowhub.eu/workflows/98?version=2

Inputs

ID Name Description Type
step1_pdb_file n/a n/a
  • File
step2_editconf_config n/a n/a
  • string
step4_grompp_genion_config n/a n/a
  • string
step5_genion_config n/a n/a
  • string
step6_grompp_min_config n/a n/a
  • string
step8_make_ndx_config n/a n/a
  • string
step9_grompp_nvt_config n/a n/a
  • string
step11_grompp_npt_config n/a n/a
  • string
step13_grompp_md_config n/a n/a
  • string
step14_mdrun_md_config n/a n/a
  • string

Steps

ID Name Description
step1_pdb2gmx Create Protein System Topology n/a
step2_editconf Create Solvent Box n/a
step3_solvate Fill the Box with Water Molecules n/a
step4_grompp_genion Add Ions - part 1 n/a
step5_genion Add Ions - part 2 n/a
step6_grompp_min Energetically Minimize the System - part 1 n/a
step7_mdrun_min Energetically Minimize the System - part 2 n/a
step8_make_ndx Generate GROMACS index file n/a
step9_grompp_nvt Equilibrate the System (NVT) - part 1 n/a
step10_mdrun_nvt Equilibrate the System (NVT) - part 2 n/a
step11_grompp_npt Equilibrate the System (NPT) - part 1 n/a
step12_mdrun_npt Equilibrate the System (NPT) - part 2 n/a
step13_grompp_md Free Molecular Dynamics Simulation - part 1 n/a
step14_mdrun_md Free Molecular Dynamics Simulation - part 2 n/a
step15_gather_outputs Archiving outputs to be returned to user n/a

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

Version History

Version 2 (latest) Created 29th Jan 2021 at 16:56 by Douglas Lowe

Trying different way of uploading the diagram (using view.commonwl.org/graph/svg, not view.commonwl.org/workflows)


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License
Apache License 2.0 (Apache-2.0)
Activity

Views: 3192   Downloads: 767

Created: 29th Jan 2021 at 16:37

Last updated: 29th Jan 2021 at 16:56

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