Workflow Type: Common Workflow Language
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Common Workflow Language example that 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). This workflow returns a resulting protein structure and simulated 3D trajectories.
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Inputs
ID | Name | Description | Type |
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step1_pdb_name | n/a | n/a |
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step1_pdb_config | n/a | n/a |
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step4_editconf_config | n/a | n/a |
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step6_gppion_config | n/a | n/a |
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step7_genion_config | n/a | n/a |
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step8_gppmin_config | n/a | n/a |
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step10_energy_min_config | n/a | n/a |
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step10_energy_min_name | n/a | n/a |
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step11_gppnvt_config | n/a | n/a |
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step13_energy_nvt_config | n/a | n/a |
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step13_energy_nvt_name | n/a | n/a |
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step14_gppnpt_config | n/a | n/a |
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step16_energy_npt_config | n/a | n/a |
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step16_energy_npt_name | n/a | n/a |
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step17_gppmd_config | n/a | n/a |
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step19_rmsfirst_config | n/a | n/a |
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step19_rmsfirst_name | n/a | n/a |
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step20_rmsexp_config | n/a | n/a |
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step20_rmsexp_name | n/a | n/a |
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step21_rgyr_config | n/a | n/a |
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step22_image_config | n/a | n/a |
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step23_dry_config | n/a | n/a |
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Steps
ID | Name | Description |
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step1_pdb | Fetch PDB Structure | Download a protein structure from the PDB database |
step2_fixsidechain | Fix Protein structure | Fix the side chains, adding any side chain atoms missing in the original structure. |
step3_pdb2gmx | Create Protein System Topology | n/a |
step4_editconf | Create Solvent Box | n/a |
step5_solvate | Fill the Box with Water Molecules | n/a |
step6_grompp_genion | Add Ions - part 1 | n/a |
step7_genion | Add Ions - part 2 | n/a |
step8_grompp_min | Energetically Minimize the System - part 1 | n/a |
step9_mdrun_min | Energetically Minimize the System - part 2 | n/a |
step10_energy_min | Energetically Minimize the System - part 3 | n/a |
step11_grompp_nvt | Equilibrate the System (NVT) - part 1 | n/a |
step12_mdrun_nvt | Equilibrate the System (NVT) - part 2 | n/a |
step13_energy_nvt | Equilibrate the System (NVT) - part 3 | n/a |
step14_grompp_npt | Equilibrate the System (NPT) - part 1 | n/a |
step15_mdrun_npt | Equilibrate the System (NPT) - part 2 | n/a |
step16_energy_npt | Equilibrate the System (NPT) - part 3 | n/a |
step17_grompp_md | Free Molecular Dynamics Simulation - part 1 | n/a |
step18_mdrun_md | Free Molecular Dynamics Simulation - part 2 | n/a |
step19_rmsfirst | Post-processing Resulting 3D Trajectory - part 1 | n/a |
step20_rmsexp | Post-processing Resulting 3D Trajectory - part 2 | n/a |
step21_rgyr | Post-processing Resulting 3D Trajectory - part 3 | n/a |
step22_image | Post-processing Resulting 3D Trajectory - part 4 | n/a |
step23_dry | Post-processing Resulting 3D Trajectory - part 5 | n/a |
Outputs
ID | Name | Description | Type |
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trr | Trajectories - Raw trajectory | Raw trajectory from the free simulation step |
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trr_imaged_dry | Trajectories - Post-processed trajectory | Post-processed trajectory, dehydrated, imaged (rotations and translations removed) and centered. |
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gro_dry | Resulting protein structure | Resulting protein structure taken from the post-processed trajectory, to be used as a topology, usually for visualization purposes. |
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gro | Structures - Raw structure | Raw structure from the free simulation step. |
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cpt | Checkpoint file | GROMACS portable checkpoint file, allowing to restore (continue) the simulation from the last step of the setup process. |
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tpr | Topologies GROMACS portable binary run | GROMACS portable binary run input file, containing the starting structure of the simulation, the molecular topology and all the simulation parameters. |
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top | GROMACS topology file | GROMACS topology file, containing the molecular topology in an ASCII readable format. |
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xvg_min | System Setup Observables - Potential Energy | Potential energy of the system during the minimization step. |
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xvg_nvt | System Setup Observables - Temperature | Temperature of the system during the NVT equilibration step. |
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xvg_npt | System Setup Observables - Pressure and density | n/a |
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xvg_rmsfirst | Simulation Analysis | Root Mean Square deviation (RMSd) throughout the whole free simulation step against the first snapshot of the trajectory (equilibrated system). |
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xvg_rmsexp | Simulation Analysis | Root Mean Square deviation (RMSd) throughout the whole free simulation step against the experimental structure (minimized system). |
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xvg_rgyr | Simulation Analysis | Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step |
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Version History
Version 3 (latest) Created 10th May 2021 at 10:00 by Robin Long
Changing CWL label to test if this corrects the workflow title.
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Version 2 Created 7th May 2021 at 16:27 by Douglas Lowe
Update to paths for BioBB tools. Taken from Git commit 46f24f0
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Version 1 (earliest) Created 16th Jun 2020 at 09:50 by Robin Long
Added/updated 1 files
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Citation
Long, R., Lowe, D., & Bayarri, G. (2021). Protein MD Setup tutorial using BioExcel Building Blocks (biobb). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.29.3
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Views: 5865 Downloads: 774
Created: 16th Jun 2020 at 09:50
Last updated: 10th Feb 2022 at 16:23
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