From 696289a1235adfd8aac1cf8f7597dc22f18cffcf Mon Sep 17 00:00:00 2001 From: gbayarri Date: Tue, 12 Mar 2024 16:31:44 +0100 Subject: [PATCH] Added references --- README.md | 2 +- biobb_wf_md_setup/docs/source/readme.md | 2 +- biobb_wf_md_setup/docs/source/tutorial.md | 4 +-- .../html/biobb_MDsetup_tutorial.web.html | 4 +-- .../notebooks/biobb_MDsetup_tutorial.ipynb | 4 +-- references.html | 26 +++++++++++++++++++ 6 files changed, 34 insertions(+), 8 deletions(-) create mode 100644 references.html diff --git a/README.md b/README.md index 79e8c6a..df383cd 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ This tutorial aims to illustrate the process of **setting up a simulation** syst * [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations. * [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories. -### Auxiliar libraries used +### Auxiliary libraries used * [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages. * [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks. diff --git a/biobb_wf_md_setup/docs/source/readme.md b/biobb_wf_md_setup/docs/source/readme.md index 79e8c6a..df383cd 100644 --- a/biobb_wf_md_setup/docs/source/readme.md +++ b/biobb_wf_md_setup/docs/source/readme.md @@ -20,7 +20,7 @@ This tutorial aims to illustrate the process of **setting up a simulation** syst * [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations. * [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories. -### Auxiliar libraries used +### Auxiliary libraries used * [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages. * [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks. diff --git a/biobb_wf_md_setup/docs/source/tutorial.md b/biobb_wf_md_setup/docs/source/tutorial.md index 3d1333f..5bd2f4d 100644 --- a/biobb_wf_md_setup/docs/source/tutorial.md +++ b/biobb_wf_md_setup/docs/source/tutorial.md @@ -13,7 +13,7 @@ This tutorial aims to illustrate the process of **setting up a simulation system - [biobb_gromacs](https://github.com/bioexcel/biobb_gromacs): Tools to setup and run Molecular Dynamics simulations. - [biobb_analysis](https://github.com/bioexcel/biobb_analysis): Tools to analyse Molecular Dynamics trajectories. -### Auxiliar libraries used +### Auxiliary libraries used * [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages. * [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks. @@ -1064,7 +1064,7 @@ Important **Output files** generated: - 1AKI_md.trr: **Final trajectory** of the MD setup protocol. - 1AKI_md.cpt: **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation. - 1AKI_gppmd.tpr: **Final tpr file**, GROMACS portable binary run input file. This file contains the starting structure of the **MD setup free MD simulation step**, together with the molecular topology and all the simulation parameters. It can be used to **extend** the simulation. - - 1AKI_genion_top.zip: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliar **include topology** files (.itp). + - 1AKI_genion_top.zip: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliary **include topology** files (.itp). **Analysis** (MD setup check) output files generated: - 1AKI_rms_first.xvg: **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**. diff --git a/biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.html b/biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.html index 3b82528..283ecca 100644 --- a/biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.html +++ b/biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.html @@ -13087,7 +13087,7 @@

Settings

biobb_gromacs: Tools to setup and run Molecular Dynamics simulations.
  • biobb_analysis: Tools to analyse Molecular Dynamics trajectories.
    • -

    Auxiliar libraries used