CWL Protein-Membrane MD analysis tutorial
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Protein-Membrane MD analysis tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb). The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the brain, which was embedded in a DPPC membrane in the MemProtMD project, which trajectory is obtained from the MDDB, where we can find it under the A01M6 accession id.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU Horizon Europe 101093290, EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

Click and drag the diagram to pan, double click or use the controls to zoom.

SEEK ID: https://workflowhub.eu/workflows/2149?version=1

DOI: 10.48546/workflowhub.workflow.2149.1

Inputs

ID Name Description Type
step1_gmx_image1_input_traj_path Input file Path to the GROMACS trajectory file.
  • File
step1_gmx_image1_input_top_path Input file Path to the GROMACS input topology file.
  • File
step1_gmx_image1_output_traj_path Output file Path to the output file.
  • string
step1_gmx_image1_config Config file Configuration file for biobb_analysis.gmx_image tool.
  • string
step2_gmx_image2_input_top_path Input file Path to the GROMACS input topology file.
  • File
step2_gmx_image2_output_traj_path Output file Path to the output file.
  • string
step2_gmx_image2_config Config file Configuration file for biobb_analysis.gmx_image tool.
  • string
step3_fatslim_membranes_input_traj_path Input file Path to the GROMACS trajectory file.
  • File
step3_fatslim_membranes_input_top_path Input file Path to the input topology file.
  • File
step3_fatslim_membranes_output_ndx_path Output file Path to the output index NDX file.
  • string
step3_fatslim_membranes_config Config file Configuration file for biobb_mem.fatslim_membranes tool.
  • string
step4_lpp_assign_leaflets_input_top_path Input file Path to the input structure or topology file.
  • File
step4_lpp_assign_leaflets_output_leaflets_path Output file Path to the output leaflet assignments.
  • string
step4_lpp_assign_leaflets_config Config file Configuration file for biobb_mem.lpp_assign_leaflets tool.
  • string
step5_lpp_zpositions1_input_top_path Input file Path to the input structure or topology file.
  • File
step5_lpp_zpositions1_output_positions_path Output file Path to the output z positions.
  • string
step5_lpp_zpositions1_config Config file Configuration file for biobb_mem.lpp_zpositions tool.
  • string
step6_lpp_zpositions2_input_top_path Input file Path to the input structure or topology file.
  • File
step6_lpp_zpositions2_output_positions_path Output file Path to the output z positions.
  • string
step6_lpp_zpositions2_config Config file Configuration file for biobb_mem.lpp_zpositions tool.
  • string
step7_gorder_aa_input_traj_path Input file Path to the input trajectory to be processed.
  • File
step7_gorder_aa_input_top_path Input file Path to the input structure or topology file.
  • File
step7_gorder_aa_output_order_path Output file Path to results of the order analysis.
  • string
step7_gorder_aa_config Config file Configuration file for biobb_mem.gorder_aa tool.
  • string
step8_fatslim_apl_input_top_path Input file Path to the input topology file.
  • File
step8_fatslim_apl_output_csv_path Output file Path to the output CSV file.
  • string
step8_fatslim_apl_config Config file Configuration file for biobb_mem.fatslim_apl tool.
  • string
step9_cpptraj_density_input_top_path Input file Path to the input structure or topology file.
  • File
step9_cpptraj_density_output_cpptraj_path Output file Path to the output processed density analysis.
  • string
step9_cpptraj_density_config Config file Configuration file for biobb_mem.cpptraj_density tool.
  • string
step10_mda_hole_input_top_path Input file Path to the input structure or topology file.
  • File
step10_mda_hole_output_hole_path Output file Path to the output HOLE analysis results.
  • string
step10_mda_hole_output_csv_path Output file Path to the output CSV file containing the radius and coordinates of the pore.
  • string
step10_mda_hole_config Config file Configuration file for biobb_mem.mda_hole tool.
  • string
step11_lpp_flip_flop_input_top_path Input file Path to the input structure or topology file.
  • File
step11_lpp_flip_flop_output_flip_flop_path Output file Path to the output flip-flop data.
  • string
step11_lpp_flip_flop_config Config file Configuration file for biobb_mem.lpp_flip_flop tool.
  • string

Steps

ID Name Description
step1_gmx_image1 gmx_image Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
step2_gmx_image2 gmx_image Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
step3_fatslim_membranes fatslim_membranes Identify membrane types and leaflets.
step4_lpp_assign_leaflets lpp_assign_leaflets Assign lipids to leaflets in a bilayer.
step5_lpp_zpositions1 lpp_zpositions Calculate the z distance in of lipids to the bilayer center.
step6_lpp_zpositions2 lpp_zpositions Calculate the z distance in of lipids to the bilayer center.
step7_gorder_aa gorder_aa Compute atomistic lipid order parameters using gorder order tool.
step8_fatslim_apl fatslim_apl Calculate the area per lipid.
step9_cpptraj_density cpptraj_density Calculates the density along an axis of a given cpptraj compatible trajectory.
step10_mda_hole mda_hole Wrapper of the MDAnalysis Hole module for analyzing hole geometry in protein channels and other macromolecular structures.
step11_lpp_flip_flop lpp_flip_flop Find flip-flop events in a lipid bilayer.

Outputs

ID Name Description Type
step1_gmx_image1_out1 output_traj_path Path to the output file.
  • File
step2_gmx_image2_out1 output_traj_path Path to the output file.
  • File
step3_fatslim_membranes_out1 output_ndx_path Path to the output index NDX file.
  • File
step4_lpp_assign_leaflets_out1 output_leaflets_path Path to the output leaflet assignments.
  • File
step5_lpp_zpositions1_out1 output_positions_path Path to the output z positions.
  • File
step6_lpp_zpositions2_out1 output_positions_path Path to the output z positions.
  • File
step7_gorder_aa_out1 output_order_path Path to results of the order analysis.
  • File
step8_fatslim_apl_out1 output_csv_path Path to the output CSV file.
  • File
step9_cpptraj_density_out1 output_cpptraj_path Path to the output processed density analysis.
  • File
step10_mda_hole_out1 output_hole_path Path to the output HOLE analysis results.
  • File
step10_mda_hole_out2 output_csv_path Path to the output CSV file containing the radius and coordinates of the pore.
  • File
step11_lpp_flip_flop_out1 output_flip_flop_path Path to the output flip-flop data.
  • File

Version History

Version 1 (earliest) Created 27th Mar 2026 at 09:54 by Genís Bayarri

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Citation
Bayarri, G., & Hospital, A. (2026). CWL Protein-Membrane MD analysis tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.2149.1
License
Apache License 2.0 (Apache-2.0)
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Views: 224   Downloads: 68

Created: 27th Mar 2026 at 09:54

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