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Tests GROMACS dcTMD free energy calculation
Perform an ensemble of targeted MD simulations of a user-specified size using the GROMACS PULL code and calculate dcTMD free energy and friction profiles for the resulting dissocation pathway. Note that pathway separation is not performed by the workflow; the user is responsible for checking the ensemble themselves.
The input protein (PDB) and ligand (SDF) files provided are parameterized by the 'Protein-ligand complex parameterization' subworkflow.
Note that the workflow uses a MDP file for configuring the TMD simulations; this
is packaged alongside the workflow as tmd.mdp.
Citations
- Steffen Wolf and Gerhard Stock (2018), Targeted Molecular Dynamics Calculations of Free Energy Profiles Using a Nonequilibrium Friction Correction, J. Chem. Theory Comput. doi:10.1021/acs.jctc.8b00835
- Steffen Wolf, Benjamin Lickert, Simon Bray and Gerhard Stock (2020), Multisecond ligand dissociation dynamics from atomistic simulations, Nat. Commun. doi:10.1038/s41467-020-16655-1
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Force field | Force field | Force field |
|
| Ligand SDF | Ligand SDF | Ligand SDF |
|
| Number of equilibration steps | Number of equilibration steps | Number of equilibration steps |
|
| Number of simulations | Number of simulations | Number of simulations in the TMD ensemble |
|
| Number of steps | Number of steps | Number of steps for the production simulation |
|
| Protein PDB | Protein PDB | Protein PDB |
|
| Protein pull group | Protein pull group | List of atom indices (separated with spaces) which make up the protein pull group |
|
| Pull group pbcatom | Pull group pbcatom | pull-group1-pbcatom - the reference atom index for the treatment of periodic boundary conditions inside the group |
|
| Pulling rate | Pulling rate | Rate to pull groups apart (nm/ps) |
|
| Salt concentration | Salt concentration | NaCl concentration (mol/dm^3) |
|
| Step length (ps) | Step length (ps) | MD step length |
|
| Temperature | Temperature | Temperature |
|
| Water model | Water model | Water model |
|
| pH to protonate ligand | pH to protonate ligand | Set to -1.0 to skip protonation |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Online data | toolshed.g2.bx.psu.edu/repos/bgruening/get_online_data/ctb_online_data_fetch/0.4 |
| 15 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 16 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 17 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 18 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 19 | Create GRO and TOP complex files | d354bc62a13564f8 |
| 20 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0 |
| 21 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 22 | GROMACS solvation and adding ions | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2021.3+galaxy0 |
| 23 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 |
| 24 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 25 | GROMACS energy minimization | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2021.3+galaxy1 |
| 26 | Parse parameter value | param_value_from_file |
| 27 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 28 | Create GROMACS index files | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_makendx/gmx_makendx/2021.3+galaxy0 |
| 29 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2 |
| 30 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 31 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 |
| 32 | Add line to file | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 33 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 34 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2 |
| 35 | dcTMD friction correction | toolshed.g2.bx.psu.edu/repos/chemteam/biomd_neqgamma/biomd_neqgamma/0.1.5.2+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Topology | Topology | n/a |
|
| Structure file (GRO format, optional) | Structure file (GRO format, optional) | n/a |
|
| GROMACS setup (ITP) on input dataset(s) | GROMACS setup (ITP) on input dataset(s) | n/a |
|
| XVG files | XVG files | n/a |
|
| XTC files | XTC files | n/a |
|
| TPR files | TPR files | n/a |
|
| GRO files | GRO files | n/a |
|
| Log | Log | n/a |
|
| Friction data | Friction data | n/a |
|
| Free energy data | Free energy data | n/a |
|
Version History
v0.1.2 (latest) Created 21st Dec 2021 at 03:01 by WorkflowHub Bot
Updated to v0.1.2
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v0.1.1 (earliest) Created 7th Dec 2021 at 03:01 by WorkflowHub Bot
Added/updated 9 files
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Views: 3839 Downloads: 355 Runs: 0
Created: 7th Dec 2021 at 03:01
Last updated: 21st Dec 2021 at 03:01
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