Example of setting up a simulation system
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

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).

Inputs

ID Name Description Type
step1_pdb_name n/a n/a
  • string
step1_pdb_config n/a n/a
  • string
step4_editconf_config n/a n/a
  • string
step6_gppion_config n/a n/a
  • string
step7_genion_config n/a n/a
  • string
step8_gppmin_config n/a n/a
  • string
step10_energy_min_config n/a n/a
  • string
step10_energy_min_name n/a n/a
  • string
step11_gppnvt_config n/a n/a
  • string
step13_energy_nvt_config n/a n/a
  • string
step13_energy_nvt_name n/a n/a
  • string
step14_gppnpt_config n/a n/a
  • string
step16_energy_npt_config n/a n/a
  • string
step16_energy_npt_name n/a n/a
  • string
step17_gppmd_config n/a n/a
  • string
step19_rmsfirst_config n/a n/a
  • string
step19_rmsfirst_name n/a n/a
  • string
step20_rmsexp_config n/a n/a
  • string
step20_rmsexp_name n/a n/a
  • string
step21_rgyr_config n/a n/a
  • string
step22_image_config n/a n/a
  • string
step23_dry_config n/a n/a
  • string

Steps

ID Name Description
step1_pdb Fetch PDB Structure n/a
step2_fixsidechain Fix Protein structure n/a
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
trr Trajectories - Raw trajectory Raw trajectory from the free simulation step
  • File
trr_imaged_dry Trajectories - Post-processed trajectory Post-processed trajectory, dehydrated, imaged (rotations and translations removed) and centered.
  • File
gro_dry Resulting protein structure Resulting protein structure taken from the post-processed trajectory, to be used as a topology, usually for visualization purposes.
  • File
gro Structures - Raw structure Raw structure from the free simulation step.
  • File
cpt Checkpoint file GROMACS portable checkpoint file, allowing to restore (continue) the simulation from the last step of the setup process.
  • File
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.
  • File
top GROMACS topology file GROMACS topology file, containing the molecular topology in an ASCII readable format.
  • File
xvg_min System Setup Observables - Potential Energy Potential energy of the system during the minimization step.
  • File
xvg_nvt System Setup Observables - Temperature Temperature of the system during the NVT equilibration step.
  • File
xvg_npt System Setup Observables - Pressure and density n/a
  • File
xvg_rmsfirst Simulation Analysis Root Mean Square deviation (RMSd) throughout the whole free simulation step against the first snapshot of the trajectory (equilibrated system).
  • File
xvg_rmsexp Simulation Analysis Root Mean Square deviation (RMSd) throughout the whole free simulation step against the experimental structure (minimized system).
  • File
xvg_rgyr Simulation Analysis Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step
  • File
Total size: 10.1 KB
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Created: 16th Jun 2020 at 08:48

Last used: 21st Oct 2021 at 14:16

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Version 1 (earliest) Created 16th Jun 2020 at 08:48 by Robin Long

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