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).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
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Inputs
ID | Name | Description | Type |
---|---|---|---|
step0_reduce_remove_hydrogens_input_path | Input file | Path to the input file. |
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step0_reduce_remove_hydrogens_output_path | Output file | Path to the output file. |
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step1_extract_molecule_output_molecule_path | Output file | Output molecule file path. |
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step00_cat_pdb_input_structure2 | Input file | Input structure 2 file path. |
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step00_cat_pdb_output_structure_path | Output file | Output protein file path. |
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step2_fix_side_chain_output_pdb_path | Output file | Output PDB file path. |
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step4_pdb2gmx_output_gro_path | Output file | Path to the output GRO file. |
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step4_pdb2gmx_output_top_zip_path | Output file | Path the output TOP topology in zip format. |
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step4_pdb2gmx_config | Config file | Configuration file for biobb_gromacs.pdb2gmx tool. |
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step5_editconf_output_gro_path | Output file | Path to the output GRO file. |
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step5_editconf_config | Config file | Configuration file for biobb_gromacs.editconf tool. |
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step6_solvate_output_gro_path | Output file | Path to the output GRO file. |
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step6_solvate_output_top_zip_path | Output file | Path the output topology in zip format. |
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step7_grompp_genion_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step7_grompp_genion_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step8_genion_output_gro_path | Output file | Path to the input structure GRO file. |
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step8_genion_output_top_zip_path | Output file | Path the output topology TOP and ITP files zipball. |
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step8_genion_config | Config file | Configuration file for biobb_gromacs.genion tool. |
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step9_grompp_min_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step9_grompp_min_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step10_mdrun_min_output_trr_path | Output file | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step10_mdrun_min_output_gro_path | Output file | Path to the output GROMACS structure GRO file. |
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step10_mdrun_min_output_edr_path | Output file | Path to the output GROMACS portable energy file EDR. |
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step10_mdrun_min_output_log_path | Output file | Path to the output GROMACS trajectory log file LOG. |
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step100_make_ndx_output_ndx_path | Output file | Path to the output index NDX file. |
|
step100_make_ndx_config | Config file | Configuration file for biobb_gromacs.make_ndx tool. |
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step11_grompp_nvt_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step11_grompp_nvt_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step12_mdrun_nvt_output_trr_path | Output file | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step12_mdrun_nvt_output_gro_path | Output file | Path to the output GROMACS structure GRO file. |
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step12_mdrun_nvt_output_edr_path | Output file | Path to the output GROMACS portable energy file EDR. |
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step12_mdrun_nvt_output_log_path | Output file | Path to the output GROMACS trajectory log file LOG. |
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step12_mdrun_nvt_output_cpt_path | Output file | Path to the output GROMACS checkpoint file CPT. |
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step13_grompp_npt_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step13_grompp_npt_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step14_mdrun_npt_output_trr_path | Output file | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step14_mdrun_npt_output_gro_path | Output file | Path to the output GROMACS structure GRO file. |
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step14_mdrun_npt_output_edr_path | Output file | Path to the output GROMACS portable energy file EDR. |
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step14_mdrun_npt_output_log_path | Output file | Path to the output GROMACS trajectory log file LOG. |
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step14_mdrun_npt_output_cpt_path | Output file | Path to the output GROMACS checkpoint file CPT. |
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step15_grompp_md_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step15_grompp_md_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step16_mdrun_md_output_trr_path | Output file | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step16_mdrun_md_output_gro_path | Output file | Path to the output GROMACS structure GRO file. |
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step16_mdrun_md_output_edr_path | Output file | Path to the output GROMACS portable energy file EDR. |
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step16_mdrun_md_output_log_path | Output file | Path to the output GROMACS trajectory log file LOG. |
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step16_mdrun_md_output_cpt_path | Output file | Path to the output GROMACS checkpoint file CPT. |
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step17_gmx_image1_output_traj_path | Output file | Path to the output file. |
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step17_gmx_image1_config | Config file | Configuration file for biobb_analysis.gmx_image tool. |
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step18_gmx_image2_output_traj_path | Output file | Path to the output file. |
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step18_gmx_image2_config | Config file | Configuration file for biobb_analysis.gmx_image tool. |
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step19_gmx_trjconv_str_output_str_path | Output file | Path to the output file. |
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step19_gmx_trjconv_str_config | Config file | Configuration file for biobb_analysis.gmx_trjconv_str tool. |
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step20_gmx_energy_output_xvg_path | Output file | Path to the XVG output file. |
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step20_gmx_energy_config | Config file | Configuration file for biobb_analysis.gmx_energy tool. |
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step21_gmx_rgyr_output_xvg_path | Output file | Path to the XVG output file. |
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step21_gmx_rgyr_config | Config file | Configuration file for biobb_analysis.gmx_rgyr tool. |
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step22_rmsd_first_output_xvg_path | Output file | Path to the XVG output file. |
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step22_rmsd_first_config | Config file | Configuration file for biobb_analysis.gmx_rms tool. |
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step23_rmsd_exp_output_xvg_path | Output file | Path to the XVG output file. |
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step23_rmsd_exp_config | Config file | Configuration file for biobb_analysis.gmx_rms tool. |
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step24_grompp_md_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step24_grompp_md_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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Steps
ID | Name | Description |
---|---|---|
step0_reduce_remove_hydrogens | reduce_remove_hydrogens | Removes hydrogen atoms to small molecules. |
step1_extract_molecule | extract_molecule | This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure. |
step00_cat_pdb | cat_pdb | Class to concat two PDB structures in a single PDB file. |
step2_fix_side_chain | fix_side_chain | 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 | make_ndx | 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 | gmx_image | Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file. |
step18_gmx_image2 | gmx_image | Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file. |
step19_gmx_trjconv_str | gmx_trjconv_str | Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms. |
step20_gmx_energy | gmx_energy | Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file. |
step21_gmx_rgyr | gmx_rgyr | 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 | gmx_rms | Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS compatible trajectory. |
step23_rmsd_exp | gmx_rms | Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS 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. |
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step1_extract_molecule_out1 | output_molecule_path | Output molecule file path. |
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step00_cat_pdb_out1 | output_structure_path | Output protein file path. |
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step2_fix_side_chain_out1 | output_pdb_path | Output PDB file path. |
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step4_pdb2gmx_out1 | output_gro_path | Path to the output GRO file. |
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step4_pdb2gmx_out2 | output_top_zip_path | Path the output TOP topology in zip format. |
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step5_editconf_out1 | output_gro_path | Path to the output GRO file. |
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step6_solvate_out1 | output_gro_path | Path to the output GRO file. |
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step6_solvate_out2 | output_top_zip_path | Path the output topology in zip format. |
|
step7_grompp_genion_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step8_genion_out1 | output_gro_path | Path to the input structure GRO file. |
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step8_genion_out2 | output_top_zip_path | Path the output topology TOP and ITP files zipball. |
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step9_grompp_min_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step10_mdrun_min_out1 | output_trr_path | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step10_mdrun_min_out2 | output_gro_path | Path to the output GROMACS structure GRO file. |
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step10_mdrun_min_out3 | output_edr_path | Path to the output GROMACS portable energy file EDR. |
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step10_mdrun_min_out4 | output_log_path | Path to the output GROMACS trajectory log file LOG. |
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step100_make_ndx_out1 | output_ndx_path | Path to the output index NDX file. |
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step11_grompp_nvt_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step12_mdrun_nvt_out1 | output_trr_path | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step12_mdrun_nvt_out2 | output_gro_path | Path to the output GROMACS structure GRO file. |
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step12_mdrun_nvt_out3 | output_edr_path | Path to the output GROMACS portable energy file EDR. |
|
step12_mdrun_nvt_out4 | output_log_path | Path to the output GROMACS trajectory log file LOG. |
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step12_mdrun_nvt_out5 | output_cpt_path | Path to the output GROMACS checkpoint file CPT. |
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step13_grompp_npt_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step14_mdrun_npt_out1 | output_trr_path | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step14_mdrun_npt_out2 | output_gro_path | Path to the output GROMACS structure GRO file. |
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step14_mdrun_npt_out3 | output_edr_path | Path to the output GROMACS portable energy file EDR. |
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step14_mdrun_npt_out4 | output_log_path | Path to the output GROMACS trajectory log file LOG. |
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step14_mdrun_npt_out5 | output_cpt_path | Path to the output GROMACS checkpoint file CPT. |
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step15_grompp_md_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step16_mdrun_md_out1 | output_trr_path | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step16_mdrun_md_out2 | output_gro_path | Path to the output GROMACS structure GRO file. |
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step16_mdrun_md_out3 | output_edr_path | Path to the output GROMACS portable energy file EDR. |
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step16_mdrun_md_out4 | output_log_path | Path to the output GROMACS trajectory log file LOG. |
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step16_mdrun_md_out5 | output_cpt_path | Path to the output GROMACS checkpoint file CPT. |
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step17_gmx_image1_out1 | output_traj_path | Path to the output file. |
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step18_gmx_image2_out1 | output_traj_path | Path to the output file. |
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step19_gmx_trjconv_str_out1 | output_str_path | Path to the output file. |
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step20_gmx_energy_out1 | output_xvg_path | Path to the XVG output file. |
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step21_gmx_rgyr_out1 | output_xvg_path | Path to the XVG output file. |
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step22_rmsd_first_out1 | output_xvg_path | Path to the XVG output file. |
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step23_rmsd_exp_out1 | output_xvg_path | Path to the XVG output file. |
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step24_grompp_md_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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Version History
Version 2 (latest) Created 7th Jun 2023 at 11:04 by Genís Bayarri
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Version 1 (earliest) Created 17th Mar 2022 at 09:18 by Genís Bayarri
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