gromacs-dctmd/main

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Workflow Type: Galaxy

Perform dcTMD free energy simulations and calculations

SEEK ID: https://workflowhub.eu/workflows/249?version=4

Inputs

ID Name Description Type
Force field Force field Force field
  • string
Ligand SDF Ligand SDF Ligand SDF
  • File
Number of equilibration steps Number of equilibration steps Number of equilibration steps
  • int
Number of simulations Number of simulations Number of simulations in the TMD ensemble
  • int
Number of steps Number of steps Number of steps for the production simulation
  • int
Protein PDB Protein PDB Protein PDB
  • File
Protein pull group Protein pull group List of atom indices (separated with spaces) which make up the protein pull group
  • string
Pull group pbcatom Pull group pbcatom pull-group1-pbcatom - the reference atom index for the treatment of periodic boundary conditions inside the group
  • int
Pulling rate Pulling rate Rate to pull groups apart (nm/ps)
  • float
Salt concentration Salt concentration NaCl concentration (mol/dm^3)
  • float
Step length (ps) Step length (ps) MD step length
  • float
Temperature Temperature Temperature
  • string
Water model Water model Water model
  • string
pH to protonate ligand pH to protonate ligand Set to -1.0 to skip protonation
  • float?

Steps

ID Name Description
9 Online data toolshed.g2.bx.psu.edu/repos/bgruening/get_online_data/ctb_online_data_fetch/0.4
15 Create GRO and TOP complex files n/a
16 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0
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 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
20 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
21 GROMACS solvation and adding ions toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2022+galaxy0
22 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
23 Add line to file toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
24 GROMACS energy minimization toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2022+galaxy0
25 Parse parameter value param_value_from_file
26 Add line to file toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
27 Create GROMACS index files toolshed.g2.bx.psu.edu/repos/chemteam/gmx_makendx/gmx_makendx/2022+galaxy0
28 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0
29 Add line to file toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
30 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
31 Add line to file toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
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/2022+galaxy0
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
  • File
Structure file (GRO format, optional) Structure file (GRO format, optional) n/a
  • File
GROMACS setup (ITP) on input dataset(s) GROMACS setup (ITP) on input dataset(s) n/a
  • File
XVG files XVG files n/a
  • File
XTC files XTC files n/a
  • File
TPR files TPR files n/a
  • File
GRO files GRO files n/a
  • File
Log Log n/a
  • File
Friction data Friction data n/a
  • File
Free energy data Free energy data n/a
  • File

Version History

v0.1.5 (latest) Created 24th Apr 2025 at 03:01 by WorkflowHub Bot

Updated to v0.1.5


Frozen v0.1.5 f0d2a4a

v0.1.4 Created 24th Apr 2025 at 03:01 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 2fa8742

v0.1.2 Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.2


Open master 716c90c

v0.1.1 (earliest) Created 7th Dec 2021 at 03:01 by WorkflowHub Bot

Added/updated 9 files


Frozen master f3dd2e9
help Creators and Submitter
Creator
  • Simon Bray
Additional credit

Simon Bray

Submitter
Tools
ChemicalToolbox
Gromacs
License
MIT License (MIT)
Activity

Views: 7303   Downloads: 5102   Runs: 0

Created: 7th Dec 2021 at 03:01

Last updated: 24th Apr 2025 at 03:01

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