Protein Ligand Complex 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 in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).
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 |
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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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step2_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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step4_fix_side_chain_output_pdb_path | Output file | Output PDB file path. |
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step5_pdb2gmx_output_gro_path | Output file | Path to the output GRO file. |
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step5_pdb2gmx_output_top_zip_path | Output file | Path the output TOP topology in zip format. |
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step5_pdb2gmx_config | Config file | Configuration file for biobb_gromacs.pdb2gmx tool. |
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step9_make_ndx_input_structure_path | Input file | Path to the input GRO/PDB/TPR file. |
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step9_make_ndx_output_ndx_path | Output file | Path to the output index NDX file. |
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step9_make_ndx_config | Config file | Configuration file for biobb_gromacs.make_ndx tool. |
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step10_genrestr_input_structure_path | Input file | Path to the input structure PDB, GRO or TPR format. |
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step10_genrestr_output_itp_path | Output file | Path the output ITP topology file with restrains. |
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step10_genrestr_config | Config file | Configuration file for biobb_gromacs.genrestr tool. |
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step11_gmx_trjconv_str_protein_output_str_path | Output file | Path to the output file. |
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step11_gmx_trjconv_str_protein_config | Config file | Configuration file for biobb_analysis.gmx_trjconv_str tool. |
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step12_gmx_trjconv_str_ligand_input_structure_path | Input file | Path to the input structure file. |
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step12_gmx_trjconv_str_ligand_input_top_path | Input file | Path to the GROMACS input topology file. |
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step12_gmx_trjconv_str_ligand_output_str_path | Output file | Path to the output file. |
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step12_gmx_trjconv_str_ligand_config | Config file | Configuration file for biobb_analysis.gmx_trjconv_str tool. |
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step13_cat_pdb_hydrogens_output_structure_path | Output file | Output protein file path. |
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step14_append_ligand_input_itp_path | Input file | Path to the ligand ITP file to be inserted in the topology. |
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step14_append_ligand_output_top_zip_path | Output file | Path/Name the output topology TOP and ITP files zipball. |
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step14_append_ligand_config | Config file | Configuration file for biobb_gromacs.append_ligand tool. |
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step15_editconf_output_gro_path | Output file | Path to the output GRO file. |
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step15_editconf_config | Config file | Configuration file for biobb_gromacs.editconf tool. |
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step16_solvate_output_gro_path | Output file | Path to the output GRO file. |
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step16_solvate_output_top_zip_path | Output file | Path the output topology in zip format. |
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step17_grompp_genion_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step17_grompp_genion_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step18_genion_output_gro_path | Output file | Path to the input structure GRO file. |
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step18_genion_output_top_zip_path | Output file | Path the output topology TOP and ITP files zipball. |
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step18_genion_config | Config file | Configuration file for biobb_gromacs.genion tool. |
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step19_grompp_min_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step19_grompp_min_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step20_mdrun_min_output_trr_path | Output file | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step20_mdrun_min_output_gro_path | Output file | Path to the output GROMACS structure GRO file. |
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step20_mdrun_min_output_edr_path | Output file | Path to the output GROMACS portable energy file EDR. |
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step20_mdrun_min_output_log_path | Output file | Path to the output GROMACS trajectory log file LOG. |
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step21_gmx_energy_min_output_xvg_path | Output file | Path to the XVG output file. |
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step21_gmx_energy_min_config | Config file | Configuration file for biobb_analysis.gmx_energy tool. |
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step22_make_ndx_output_ndx_path | Output file | Path to the output index NDX file. |
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step22_make_ndx_config | Config file | Configuration file for biobb_gromacs.make_ndx tool. |
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step23_grompp_nvt_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step23_grompp_nvt_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step24_mdrun_nvt_output_trr_path | Output file | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step24_mdrun_nvt_output_gro_path | Output file | Path to the output GROMACS structure GRO file. |
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step24_mdrun_nvt_output_edr_path | Output file | Path to the output GROMACS portable energy file EDR. |
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step24_mdrun_nvt_output_log_path | Output file | Path to the output GROMACS trajectory log file LOG. |
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step24_mdrun_nvt_output_cpt_path | Output file | Path to the output GROMACS checkpoint file CPT. |
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step25_gmx_energy_nvt_output_xvg_path | Output file | Path to the XVG output file. |
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step25_gmx_energy_nvt_config | Config file | Configuration file for biobb_analysis.gmx_energy tool. |
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step26_grompp_npt_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step26_grompp_npt_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step27_mdrun_npt_output_trr_path | Output file | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step27_mdrun_npt_output_gro_path | Output file | Path to the output GROMACS structure GRO file. |
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step27_mdrun_npt_output_edr_path | Output file | Path to the output GROMACS portable energy file EDR. |
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step27_mdrun_npt_output_log_path | Output file | Path to the output GROMACS trajectory log file LOG. |
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step27_mdrun_npt_output_cpt_path | Output file | Path to the output GROMACS checkpoint file CPT. |
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step28_gmx_energy_npt_output_xvg_path | Output file | Path to the XVG output file. |
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step28_gmx_energy_npt_config | Config file | Configuration file for biobb_analysis.gmx_energy tool. |
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step29_grompp_md_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step29_grompp_md_config | Config file | Configuration file for biobb_gromacs.grompp tool. |
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step30_mdrun_md_output_trr_path | Output file | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step30_mdrun_md_output_gro_path | Output file | Path to the output GROMACS structure GRO file. |
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step30_mdrun_md_output_edr_path | Output file | Path to the output GROMACS portable energy file EDR. |
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step30_mdrun_md_output_log_path | Output file | Path to the output GROMACS trajectory log file LOG. |
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step30_mdrun_md_output_cpt_path | Output file | Path to the output GROMACS checkpoint file CPT. |
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step34_gmx_image_output_traj_path | Output file | Path to the output file. |
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step34_gmx_image_config | Config file | Configuration file for biobb_analysis.gmx_image tool. |
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step34b_gmx_image2_output_traj_path | Output file | Path to the output file. |
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step34b_gmx_image2_config | Config file | Configuration file for biobb_analysis.gmx_image tool. |
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step35_gmx_trjconv_str_output_str_path | Output file | Path to the output file. |
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step35_gmx_trjconv_str_config | Config file | Configuration file for biobb_analysis.gmx_trjconv_str tool. |
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step31_rmsd_first_output_xvg_path | Output file | Path to the XVG output file. |
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step31_rmsd_first_config | Config file | Configuration file for biobb_analysis.gmx_rms tool. |
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step32_rmsd_exp_output_xvg_path | Output file | Path to the XVG output file. |
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step32_rmsd_exp_config | Config file | Configuration file for biobb_analysis.gmx_rms tool. |
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step33_gmx_rgyr_output_xvg_path | Output file | Path to the XVG output file. |
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step33_gmx_rgyr_config | Config file | Configuration file for biobb_analysis.gmx_rgyr tool. |
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step36_grompp_md_output_tpr_path | Output file | Path to the output portable binary run file TPR. |
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step36_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. |
step2_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. |
step4_fix_side_chain | fix_side_chain | Reconstructs the missing side chains and heavy atoms of the given PDB file. |
step5_pdb2gmx | pdb2gmx | Creates a compressed (ZIP) GROMACS topology (TOP and ITP files) from a given PDB file. |
step9_make_ndx | make_ndx | Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file. |
step10_genrestr | genrestr | Creates a new GROMACS compressed topology applying the indicated force restrains to the given input compressed topology. |
step11_gmx_trjconv_str_protein | gmx_trjconv_str | Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms. |
step12_gmx_trjconv_str_ligand | gmx_trjconv_str | Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms. |
step13_cat_pdb_hydrogens | cat_pdb | Class to concat two PDB structures in a single PDB file. |
step14_append_ligand | append_ligand | Takes a ligand ITP file and inserts it in a topology. |
step15_editconf | editconf | Creates a GROMACS structure file (GRO) adding the information of the solvent box to the input structure file. |
step16_solvate | solvate | Creates a new compressed GROMACS topology file adding solvent molecules to a given input compressed GROMACS topology file. |
step17_grompp_genion | grompp | Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. |
step18_genion | genion | Creates a new compressed GROMACS topology adding ions until reaching the desired concentration to the input compressed GROMACS topology. |
step19_grompp_min | grompp | Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. |
step20_mdrun_min | mdrun | Performs molecular dynamics simulations from an input GROMACS TPR file. |
step21_gmx_energy_min | gmx_energy | Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file. |
step22_make_ndx | make_ndx | Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file. |
step23_grompp_nvt | grompp | Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. |
step24_mdrun_nvt | mdrun | Performs molecular dynamics simulations from an input GROMACS TPR file. |
step25_gmx_energy_nvt | gmx_energy | Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file. |
step26_grompp_npt | grompp | Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. |
step27_mdrun_npt | mdrun | Performs molecular dynamics simulations from an input GROMACS TPR file. |
step28_gmx_energy_npt | gmx_energy | Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file. |
step29_grompp_md | grompp | Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. |
step30_mdrun_md | mdrun | Performs molecular dynamics simulations from an input GROMACS TPR file. |
step34_gmx_image | gmx_image | Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file. |
step34b_gmx_image2 | gmx_image | Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file. |
step35_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. |
step31_rmsd_first | gmx_rms | Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS compatible trajectory. |
step32_rmsd_exp | gmx_rms | Wrapper of the GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS compatible trajectory. |
step33_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. |
step36_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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step2_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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step4_fix_side_chain_out1 | output_pdb_path | Output PDB file path. |
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step5_pdb2gmx_out1 | output_gro_path | Path to the output GRO file. |
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step5_pdb2gmx_out2 | output_top_zip_path | Path the output TOP topology in zip format. |
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step9_make_ndx_out1 | output_ndx_path | Path to the output index NDX file. |
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step10_genrestr_out1 | output_itp_path | Path the output ITP topology file with restrains. |
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step11_gmx_trjconv_str_protein_out1 | output_str_path | Path to the output file. |
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step12_gmx_trjconv_str_ligand_out1 | output_str_path | Path to the output file. |
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step13_cat_pdb_hydrogens_out1 | output_structure_path | Output protein file path. |
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step14_append_ligand_out1 | output_top_zip_path | Path/Name the output topology TOP and ITP files zipball. |
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step15_editconf_out1 | output_gro_path | Path to the output GRO file. |
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step16_solvate_out1 | output_gro_path | Path to the output GRO file. |
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step16_solvate_out2 | output_top_zip_path | Path the output topology in zip format. |
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step17_grompp_genion_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step18_genion_out1 | output_gro_path | Path to the input structure GRO file. |
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step18_genion_out2 | output_top_zip_path | Path the output topology TOP and ITP files zipball. |
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step19_grompp_min_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step20_mdrun_min_out1 | output_trr_path | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step20_mdrun_min_out2 | output_gro_path | Path to the output GROMACS structure GRO file. |
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step20_mdrun_min_out3 | output_edr_path | Path to the output GROMACS portable energy file EDR. |
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step20_mdrun_min_out4 | output_log_path | Path to the output GROMACS trajectory log file LOG. |
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step21_gmx_energy_min_out1 | output_xvg_path | Path to the XVG output file. |
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step22_make_ndx_out1 | output_ndx_path | Path to the output index NDX file. |
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step23_grompp_nvt_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step24_mdrun_nvt_out1 | output_trr_path | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step24_mdrun_nvt_out2 | output_gro_path | Path to the output GROMACS structure GRO file. |
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step24_mdrun_nvt_out3 | output_edr_path | Path to the output GROMACS portable energy file EDR. |
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step24_mdrun_nvt_out4 | output_log_path | Path to the output GROMACS trajectory log file LOG. |
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step24_mdrun_nvt_out5 | output_cpt_path | Path to the output GROMACS checkpoint file CPT. |
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step25_gmx_energy_nvt_out1 | output_xvg_path | Path to the XVG output file. |
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step26_grompp_npt_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step27_mdrun_npt_out1 | output_trr_path | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step27_mdrun_npt_out2 | output_gro_path | Path to the output GROMACS structure GRO file. |
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step27_mdrun_npt_out3 | output_edr_path | Path to the output GROMACS portable energy file EDR. |
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step27_mdrun_npt_out4 | output_log_path | Path to the output GROMACS trajectory log file LOG. |
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step27_mdrun_npt_out5 | output_cpt_path | Path to the output GROMACS checkpoint file CPT. |
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step28_gmx_energy_npt_out1 | output_xvg_path | Path to the XVG output file. |
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step29_grompp_md_out1 | output_tpr_path | Path to the output portable binary run file TPR. |
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step30_mdrun_md_out1 | output_trr_path | Path to the GROMACS uncompressed raw trajectory file TRR. |
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step30_mdrun_md_out2 | output_gro_path | Path to the output GROMACS structure GRO file. |
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step30_mdrun_md_out3 | output_edr_path | Path to the output GROMACS portable energy file EDR. |
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step30_mdrun_md_out4 | output_log_path | Path to the output GROMACS trajectory log file LOG. |
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step30_mdrun_md_out5 | output_cpt_path | Path to the output GROMACS checkpoint file CPT. |
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step34_gmx_image_out1 | output_traj_path | Path to the output file. |
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step34b_gmx_image2_out1 | output_traj_path | Path to the output file. |
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step35_gmx_trjconv_str_out1 | output_str_path | Path to the output file. |
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step31_rmsd_first_out1 | output_xvg_path | Path to the XVG output file. |
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step32_rmsd_exp_out1 | output_xvg_path | Path to the XVG output file. |
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step33_gmx_rgyr_out1 | output_xvg_path | Path to the XVG output file. |
|
step36_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 11:54 by Genís Bayarri
Updated workflow descriptors
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Version 1 (earliest) Created 10th Jan 2022 at 11:52 by Genís Bayarri
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Created: 10th Jan 2022 at 11:52
Last updated: 17th Mar 2022 at 09:54
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