Example of setting up a simulation system

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

Example of setting up a simulation system
Version 1

Inputs

Steps

Outputs

Version History

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

Creators

Submitter

Example of setting up a simulation system Version 1

Inputs

Steps

Outputs

Version History

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

Creators

Submitter

Related items

Example of setting up a simulation system
Version 1