CWL Protein MD Setup tutorial
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Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

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 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/279?version=1

DOI: 10.48546/workflowhub.workflow.279.1

Inputs

ID	Name	Description	Type
step0_reduce_remove_hydrogens_input_path	n/a	n/a	File
step0_reduce_remove_hydrogens_output_path	n/a	n/a	string
step1_extract_molecule_output_molecule_path	n/a	n/a	string
step00_cat_pdb_input_structure2	n/a	n/a	File
step00_cat_pdb_output_structure_path	n/a	n/a	string
step2_fix_side_chain_output_pdb_path	n/a	n/a	string
step4_pdb2gmx_config	n/a	n/a	string
step4_pdb2gmx_output_gro_path	n/a	n/a	string
step4_pdb2gmx_output_top_zip_path	n/a	n/a	string
step5_editconf_config	n/a	n/a	string
step5_editconf_output_gro_path	n/a	n/a	string
step6_solvate_output_gro_path	n/a	n/a	string
step6_solvate_output_top_zip_path	n/a	n/a	string
step7_grompp_genion_config	n/a	n/a	string
step7_grompp_genion_output_tpr_path	n/a	n/a	string
step8_genion_config	n/a	n/a	string
step8_genion_output_gro_path	n/a	n/a	string
step8_genion_output_top_zip_path	n/a	n/a	string
step9_grompp_min_config	n/a	n/a	string
step9_grompp_min_output_tpr_path	n/a	n/a	string
step10_mdrun_min_output_trr_path	n/a	n/a	string
step10_mdrun_min_output_gro_path	n/a	n/a	string
step10_mdrun_min_output_edr_path	n/a	n/a	string
step10_mdrun_min_output_log_path	n/a	n/a	string
step100_make_ndx_config	n/a	n/a	string
step100_make_ndx_output_ndx_path	n/a	n/a	string
step11_grompp_nvt_config	n/a	n/a	string
step11_grompp_nvt_output_tpr_path	n/a	n/a	string
step12_mdrun_nvt_output_trr_path	n/a	n/a	string
step12_mdrun_nvt_output_gro_path	n/a	n/a	string
step12_mdrun_nvt_output_edr_path	n/a	n/a	string
step12_mdrun_nvt_output_log_path	n/a	n/a	string
step12_mdrun_nvt_output_cpt_path	n/a	n/a	string
step13_grompp_npt_config	n/a	n/a	string
step13_grompp_npt_output_tpr_path	n/a	n/a	string
step14_mdrun_npt_output_trr_path	n/a	n/a	string
step14_mdrun_npt_output_gro_path	n/a	n/a	string
step14_mdrun_npt_output_edr_path	n/a	n/a	string
step14_mdrun_npt_output_log_path	n/a	n/a	string
step14_mdrun_npt_output_cpt_path	n/a	n/a	string
step15_grompp_md_config	n/a	n/a	string
step15_grompp_md_output_tpr_path	n/a	n/a	string
step16_mdrun_md_output_trr_path	n/a	n/a	string
step16_mdrun_md_output_gro_path	n/a	n/a	string
step16_mdrun_md_output_edr_path	n/a	n/a	string
step16_mdrun_md_output_log_path	n/a	n/a	string
step16_mdrun_md_output_cpt_path	n/a	n/a	string
step17_gmx_image1_config	n/a	n/a	string
step17_gmx_image1_output_traj_path	n/a	n/a	string
step18_gmx_image2_config	n/a	n/a	string
step18_gmx_image2_output_traj_path	n/a	n/a	string
step19_gmx_trjconv_str_config	n/a	n/a	string
step19_gmx_trjconv_str_output_str_path	n/a	n/a	string
step20_gmx_energy_config	n/a	n/a	string
step20_gmx_energy_output_xvg_path	n/a	n/a	string
step21_gmx_rgyr_config	n/a	n/a	string
step21_gmx_rgyr_output_xvg_path	n/a	n/a	string
step22_rmsd_first_config	n/a	n/a	string
step22_rmsd_first_output_xvg_path	n/a	n/a	string
step23_rmsd_exp_config	n/a	n/a	string
step23_rmsd_exp_output_xvg_path	n/a	n/a	string
step24_grompp_md_config	n/a	n/a	string
step24_grompp_md_output_tpr_path	n/a	n/a	string

Steps

ID	Name	Description
step0_reduce_remove_hydrogens	ReduceRemoveHydrogens	Removes hydrogen atoms to small molecules.
step1_extract_molecule	ExtractMolecule	This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.
step00_cat_pdb	CatPDB	Class to concat two PDB structures in a single PDB file.
step2_fix_side_chain	FixSideChain	Reconstructs the missing side chains and heavy atoms of the given PDB file.
step4_pdb2gmx	Pdb2gmx	Creates a compressed (ZIP) GROMACS topology (TOP and ITP files) from a given PDB file.
step5_editconf	Editconf	Creates a GROMACS structure file (GRO) adding the information of the solvent box to the input structure file.
step6_solvate	Solvate	Creates a new compressed GROMACS topology file adding solvent molecules to a given input compressed GROMACS topology file.
step7_grompp_genion	Grompp	Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step8_genion	Genion	Creates a new compressed GROMACS topology adding ions until reaching the desired concentration to the input compressed GROMACS topology.
step9_grompp_min	Grompp	Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step10_mdrun_min	Mdrun	Performs molecular dynamics simulations from an input GROMACS TPR file.
step100_make_ndx	MakeNdx	Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file.
step11_grompp_nvt	Grompp	Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step12_mdrun_nvt	Mdrun	Performs molecular dynamics simulations from an input GROMACS TPR file.
step13_grompp_npt	Grompp	Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step14_mdrun_npt	Mdrun	Performs molecular dynamics simulations from an input GROMACS TPR file.
step15_grompp_md	Grompp	Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.
step16_mdrun_md	Mdrun	Performs molecular dynamics simulations from an input GROMACS TPR file.
step17_gmx_image1	GMXImage	Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
step18_gmx_image2	GMXImage	Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
step19_gmx_trjconv_str	GMXTrjconvStr	Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.
step20_gmx_energy	GMXEnergy	Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.
step21_gmx_rgyr	GMXRgyr	Wrapper of the GROMACS gyrate module for computing the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.
step22_rmsd_first	GMXRms	Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step23_rmsd_exp	GMXRms	Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step24_grompp_md	Grompp	Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.

Outputs

ID	Name	Description	Type
step0_reduce_remove_hydrogens_out1	output_path	Path to the output file	File
step1_extract_molecule_out1	output_molecule_path	Output molecule file path	File
step00_cat_pdb_out1	output_structure_path	Output protein file path	File
step2_fix_side_chain_out1	output_pdb_path	Output PDB file path	File
step4_pdb2gmx_out1	output_gro_path	Path to the output GRO file	File
step4_pdb2gmx_out2	output_top_zip_path	Path the output TOP topology in zip format	File
step5_editconf_out1	output_gro_path	Path to the output GRO file	File
step6_solvate_out1	output_gro_path	Path to the output GRO file	File
step6_solvate_out2	output_top_zip_path	Path the output topology in zip format	File
step7_grompp_genion_out1	output_tpr_path	Path to the output portable binary run file TPR	File
step8_genion_out1	output_gro_path	Path to the input structure GRO file	File
step8_genion_out2	output_top_zip_path	Path the output topology TOP and ITP files zipball	File
step9_grompp_min_out1	output_tpr_path	Path to the output portable binary run file TPR	File
step10_mdrun_min_out1	output_trr_path	Path to the GROMACS uncompressed raw trajectory file TRR	File
step10_mdrun_min_out2	output_gro_path	Path to the output GROMACS structure GRO file	File
step10_mdrun_min_out3	output_edr_path	Path to the output GROMACS portable energy file EDR	File
step10_mdrun_min_out4	output_log_path	Path to the output GROMACS trajectory log file LOG	File
step100_make_ndx_out1	output_ndx_path	Path to the output index NDX file	File
step11_grompp_nvt_out1	output_tpr_path	Path to the output portable binary run file TPR	File
step12_mdrun_nvt_out1	output_trr_path	Path to the GROMACS uncompressed raw trajectory file TRR	File
step12_mdrun_nvt_out2	output_gro_path	Path to the output GROMACS structure GRO file	File
step12_mdrun_nvt_out3	output_edr_path	Path to the output GROMACS portable energy file EDR	File
step12_mdrun_nvt_out4	output_log_path	Path to the output GROMACS trajectory log file LOG	File
step12_mdrun_nvt_out5	output_cpt_path	Path to the output GROMACS checkpoint file CPT	File
step13_grompp_npt_out1	output_tpr_path	Path to the output portable binary run file TPR	File
step14_mdrun_npt_out1	output_trr_path	Path to the GROMACS uncompressed raw trajectory file TRR	File
step14_mdrun_npt_out2	output_gro_path	Path to the output GROMACS structure GRO file	File
step14_mdrun_npt_out3	output_edr_path	Path to the output GROMACS portable energy file EDR	File
step14_mdrun_npt_out4	output_log_path	Path to the output GROMACS trajectory log file LOG	File
step14_mdrun_npt_out5	output_cpt_path	Path to the output GROMACS checkpoint file CPT	File
step15_grompp_md_out1	output_tpr_path	Path to the output portable binary run file TPR	File
step16_mdrun_md_out1	output_trr_path	Path to the GROMACS uncompressed raw trajectory file TRR	File
step16_mdrun_md_out2	output_gro_path	Path to the output GROMACS structure GRO file	File
step16_mdrun_md_out3	output_edr_path	Path to the output GROMACS portable energy file EDR	File
step16_mdrun_md_out4	output_log_path	Path to the output GROMACS trajectory log file LOG	File
step16_mdrun_md_out5	output_cpt_path	Path to the output GROMACS checkpoint file CPT	File
step17_gmx_image1_out1	output_traj_path	Path to the output file	File
step18_gmx_image2_out1	output_traj_path	Path to the output file	File
step19_gmx_trjconv_str_out1	output_str_path	Path to the output file	File
step20_gmx_energy_out1	output_xvg_path	Path to the XVG output file	File
step21_gmx_rgyr_out1	output_xvg_path	Path to the XVG output file	File
step22_rmsd_first_out1	output_xvg_path	Path to the XVG output file	File
step23_rmsd_exp_out1	output_xvg_path	Path to the XVG output file	File
step24_grompp_md_out1	output_tpr_path	Path to the output portable binary run file TPR	File