Skip to content

Update GROMACS tutorial #6405

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 8 commits into
base: main
Choose a base branch
from
Open

Update GROMACS tutorial #6405

Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
5e7eca7
Update tutorial.md
Swathi266 Oct 8, 2025
ab09f8d
Update tutorial.md
Swathi266 Oct 8, 2025
3344bed
Update tutorial.md
Swathi266 Oct 8, 2025
eaa9444
Update tutorial.md
Swathi266 Oct 9, 2025
033268e
Update tutorial.md
Swathi266 Oct 9, 2025
5aa788f
fix lint warnings
shiltemann Nov 6, 2025
b6e0a92
rename is not a parameter but a separate action
shiltemann Nov 6, 2025
f848ee3
Merge branch 'main' into patch-22
shiltemann Nov 6, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
34 changes: 19 additions & 15 deletions topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ Multiple packages exist for performing MD simulations. One of the most popular i
This is a introductory guide to using GROMACS ({% cite abraham15 %}) in Galaxy to prepare and perform molecular dynamics on a small protein. For the tutorial, we will perform our simulations on hen egg white lysozyme.

> <comment-title>More information</comment-title>
> This guide is based on the GROMACS tutorial provided by Justin Lemkul [here](http://www.mdtutorials.com/gmx/lysozyme/index.html) - please consult it if you are interested in a more detailed, technical guide to GROMACS.
> This guide is based on the [GROMACS tutorial provided by Justin Lemkul](http://www.mdtutorials.com/gmx/lysozyme/index.html) - please consult it if you are interested in a more detailed, technical guide to GROMACS.
{: .comment}

> <agenda-title></agenda-title>
Expand Down Expand Up @@ -81,6 +81,7 @@ A prepared file is available via Zenodo. Alternatively, you can prepare the file
> - *"Select lines from"*: uploaded PDB file
> - *"that"*: `Don't Match`
> - *"Regular Expression"*: `HETATM`
> 4. {% icon galaxy-pencil %} **Rename the dataset** to `1AKI_clean.pdb`
>
{: .hands_on}

Expand Down Expand Up @@ -171,7 +172,7 @@ The next stage is protein solvation, performed using **GROMACS solvation and add

To remove any steric clashes or unusual geometry which would artificially raise the energy of the system, we must relax the structure by running an energy minimization (EM) algorithm.

Here, and in the later steps, two options are presented under 'Parameter input'. Firstly, the default setting, which we will use for this tutorial, requires options to be selected through the Galaxy interface. Alternatively, you can choose to upload an MDP (molecular dynamics parameters) file to define the simulation parameters. Using your own MDP file will allow greater customization, as not all parameters are implemented in Galaxy (yet); however, it requires a more advanced knowledge of GROMACS. Description of all parameters can be found [here](http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html).
Here, and in the later steps, two options are presented under 'Parameter input'. Firstly, the default setting, which we will use for this tutorial, requires options to be selected through the Galaxy interface. Alternatively, you can choose to upload an MDP (molecular dynamics parameters) file to define the simulation parameters. Using your own MDP file will allow greater customization, as not all parameters are implemented in Galaxy (yet); however, it requires a more advanced knowledge of GROMACS. Description of all parameters can be found [in the GROMACS manual](http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html).

> <hands-on-title>energy minimization</hands-on-title>
>
Expand Down Expand Up @@ -203,16 +204,18 @@ Firstly, we perform equilibration using classical NVT dynamics.

> <hands-on-title>NVT dynamics</hands-on-title>
>
> {% tool [GROMACS simulation](toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1) %} with the following parameters:
> {% tool [GROMACS simulation](toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0) %} with the following parameters:
> - {% icon param-file %} *"GRO structure file"*: GRO structure file
> - {% icon param-file %} *"Topology (TOP) file"*: Topology
> - *"Use a checkpoint (CPT) file"*: `No CPT input`
> - *"Produce a checkpoint (CPT) file"*: `Produce CPT output`
> - *"Apply position restraints"*: `Apply position restraints`
> - {% icon param-file %} *"Position restraint file"*: Position restraint file produced by 'Setup' tool.
> - *"Ensemble"*: `Isothermal-isochoric ensemble (NVT).`
> - *"Inputs"*
> - *"Checkpoint (CPT) file"*: `Nothing selected`
> - {% icon param-file %} *"Position restraint file"*: Position restraint file produced by 'Setup' tool.
> - *"Outputs"*
> - *"Trajectory output"*: `Return no trajectory output` (we are not interested in how the system evolves to the equilibrated state, merely the final structure)
> - *"Structure output"*: `Return .gro file`
> - *"Produce a checkpoint (CPT) file"*: `Produce CPT output`
> - *"Settings"*
> - *"Ensemble"*: `Isothermal-isochoric ensemble (NVT).`
> - *"Parameter input"*: `Use default (partially customisable) setting`
> - *"Choice of integrator"*: `A leap-frog algorithm for integrating Newton’s equations of motion` (A basic leap-frog integrator)
> - *"Bond constraints"*: `Bonds with H-atoms` (bonds involving H are constrained)
Expand All @@ -235,17 +238,18 @@ Note that we can continue where the last simulation left off (with new parameter

> <hands-on-title>NPT dynamics</hands-on-title>
>
> {% tool [GROMACS simulation](toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1) %} with the following parameters:
> {% tool [GROMACS simulation](toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0) %} with the following parameters:
> - {% icon param-file %} *"GRO structure file"*: GRO structure file
> - {% icon param-file %} *"Topology (TOP) file"*: Topology
> - *"Use a checkpoint (CPT) file"*: `Continue simulation from a CPT file.`
> - *"Inputs"*
> - {% icon param-file %} *"Checkpoint (CPT) file"*: Checkpoint file produced by NVT equilibration
> - *"Produce a checkpoint (CPT) file"*: `Produce CPT output`
> - *"Apply position restraints"*: `No position restraints`
> - {% icon param-file %} *"Position restraint file"*: None
> - *"Ensemble"*: `Isothermal-isobaric ensemble (NPT).`
> - {% icon param-file %} *"Position restraint (ITP) file"*: None
> - *"Outputs"*
> - *"Trajectory output"*: `Return no trajectory output`
> - *"Structure output"*: `Return .gro file`
> - *"Produce a checkpoint (CPT) file"*: `Produce CPT output`
> - *"Settings"*
> - *"Ensemble"*: `Isothermal-isobaric ensemble (NPT).`
> - *"Parameter input"*: `Use default (partially customisable) setting`
> - *"Choice of integrator"*: `A leap-frog algorithm for integrating Newton’s equations of motion` (A basic leap-frog integrator)
> - *"Bond constraints"*: `Bonds with H-atoms` (bonds involving H are constrained)
Expand Down Expand Up @@ -276,7 +280,7 @@ Now that equilibration is complete, we can release the position restraints. We a

> <hands-on-title>Production simulation</hands-on-title>
>
> 1. {% tool [GROMACS simulation](toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1) %} with the following parameters:
> 1. {% tool [GROMACS simulation](toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0) %} with the following parameters:
> - {% icon param-file %} *"GRO structure file"*: GRO structure file
> - {% icon param-file %} *"Topology (TOP) file"*: Topology
> - *"Use a checkpoint (CPT) file"*: `Continue simulation from a CPT file.`
Expand Down