From 5e7eca7044ad7bd8a2be8e2c91b139fe25848de2 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Wed, 8 Oct 2025 17:13:21 +0530 Subject: [PATCH 1/7] Update tutorial.md --- .../tutorials/md-simulation-gromacs/tutorial.md | 1 + 1 file changed, 1 insertion(+) diff --git a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md index e92e65c2d075c1..180ab01ccb007a 100644 --- a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md +++ b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md @@ -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` +> - *"Rename the dataset"*: `1AKI_clean.pdb` > {: .hands_on} From ab09f8d10794e90241b42a878048a4f74d9f8328 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Wed, 8 Oct 2025 22:50:03 +0530 Subject: [PATCH 2/7] Update tutorial.md --- .../tutorials/md-simulation-gromacs/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md index 180ab01ccb007a..8644c3481ccb87 100644 --- a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md +++ b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md @@ -236,7 +236,7 @@ Note that we can continue where the last simulation left off (with new parameter > NPT dynamics > -> {% 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.` From 3344bed59057db2d9d753d4aa58ad8d207f9d7c7 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Wed, 8 Oct 2025 23:12:07 +0530 Subject: [PATCH 3/7] Update tutorial.md --- .../tutorials/md-simulation-gromacs/tutorial.md | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md index 8644c3481ccb87..51ae2aa525c9f7 100644 --- a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md +++ b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md @@ -207,13 +207,15 @@ Firstly, we perform equilibration using classical NVT dynamics. > {% tool [GROMACS simulation](toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1) %} 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) From eaa9444a7f8ac4d0baaffe6607f53923d5736036 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:51:17 +0530 Subject: [PATCH 4/7] Update tutorial.md --- .../tutorials/md-simulation-gromacs/tutorial.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md index 51ae2aa525c9f7..b7fd417b166dd6 100644 --- a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md +++ b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md @@ -241,14 +241,15 @@ Note that we can continue where the last simulation left off (with new parameter > {% 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) From 033268e0f0a4d02c217dc054ea70ad51be9f77bc Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:53:23 +0530 Subject: [PATCH 5/7] Update tutorial.md --- .../tutorials/md-simulation-gromacs/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md index b7fd417b166dd6..a1a0f16c555f8e 100644 --- a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md +++ b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md @@ -204,7 +204,7 @@ Firstly, we perform equilibration using classical NVT dynamics. > NVT dynamics > -> {% 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 > - *"Inputs"* @@ -280,7 +280,7 @@ Now that equilibration is complete, we can release the position restraints. We a > Production simulation > -> 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.` From 5aa788fe9926847dacb365e691884225811c251f Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 6 Nov 2025 15:36:19 +0100 Subject: [PATCH 6/7] fix lint warnings --- .../tutorials/md-simulation-gromacs/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md index a1a0f16c555f8e..fb0014f8de2929 100644 --- a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md +++ b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md @@ -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. > More information -> 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} > @@ -172,7 +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). > energy minimization > From b6e0a922f683a58eaf3ada81aa2714438aecc8f3 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 6 Nov 2025 15:37:33 +0100 Subject: [PATCH 7/7] rename is not a parameter but a separate action --- .../tutorials/md-simulation-gromacs/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md index fb0014f8de2929..e30edafb2d60e3 100644 --- a/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md +++ b/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md @@ -81,7 +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` -> - *"Rename the dataset"*: `1AKI_clean.pdb` +> 4. {% icon galaxy-pencil %} **Rename the dataset** to `1AKI_clean.pdb` > {: .hands_on}