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mkdocs.yml
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# Project information
site_name: gmx_MMPBSA Documentation
site_url: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/
site_author: Mario S. and Mario E. Valdés-Tresanco
site_description: >-
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS
files
# Repository
repo_name: gmx_MMPBSA
repo_url: https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA
edit_uri: ""
# Copyright
copyright: Copyright © 2020 - 2022 MS. and ME. Valdés-Tresanco
# Configuration
theme:
name: material
logo: assets/logo_white_border.svg
custom_dir: docs/overrides
# 404 page
static_templates:
- 404.html
# Don't include MkDocs' JavaScript
include_search_page: false
search_index_only: true
# Default values, taken from mkdocs_theme.yml
language: en
features:
- content.code.annotate
- content.tabs.link
# - header.autohide
# - navigation.expand
# - navigation.indexes
# - navigation.instant
- navigation.expand
- navigation.sections
- navigation.tabs
- navigation.top
# - navigation.tracking
- search.highlight
# - search.share
- search.suggest
# - header.autohide
- toc.integrate
palette:
- scheme: default
primary: black
accent: black
toggle:
icon: material/weather-sunny
name: Switch to dark mode
- scheme: slate
primary: black
accent: black
toggle:
icon: material/weather-night
name: Switch to light mode
# - scheme: default
# primary: black
# accent: black
# toggle:
# icon: material/weather-sunny
# name: Switch to dark mode
# - scheme: slate
# primary: black
# accent: black
# toggle:
# icon: material/weather-night
# name: Switch to light mode
font:
text: Roboto
code: Roboto Mono
favicon: assets/logo.svg
icon:
logo: logo
# Plugins
plugins:
- search
- git-revision-date-localized:
type: datetime
enable_creation_date: true
- minify:
minify_html: true
# Customization
extra:
analytics:
provider: google
property: !ENV GOOGLE_ANALYTICS_KEY
social:
- icon: fontawesome/brands/github
link: https://github.com/Valdes-Tresanco-MS
version:
provider: mike
# Extensions
markdown_extensions:
- admonition
- abbr
- attr_list
- def_list
- footnotes
- meta
- md_in_html
- toc:
permalink: true
- pymdownx.arithmatex:
generic: true
- pymdownx.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.critic
- pymdownx.details
- pymdownx.emoji:
emoji_index: !!python/name:materialx.emoji.twemoji
emoji_generator: !!python/name:materialx.emoji.to_svg
- pymdownx.highlight:
anchor_linenums: true
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.magiclink:
repo_url_shorthand: true
user: Valdes-Tresanco-MS
repo: gmx_MMPBSA
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- pymdownx.tabbed:
alternate_style: true
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
# Page tree
nav:
- Home: index.md
- Getting started:
- Getting started: getting-started.md
- Introduction: introduction.md
- gmx_MMPBSA in a nutshell: summary.md
- gmx_MMPBSA vs other programs: versus.md
- Installation: installation.md
- gmx_MMPBSA:
- How gmx_MMPBSA works: howworks.md
- Command-line: gmx_MMPBSA_command-line.md
- Running gmx_MMPBSA: gmx_MMPBSA_running.md
- The input file: input_file.md
- The output file: output.md
- Python API: api.md
- gmx_MMPBSA_ana:
- gmx_MMPBSA_ana: analyzer.md
- Command-line: gmx_MMPBSA_ana_command-line.md
- Running gmx_MMPBSA_ana: gmx_MMPBSA_ana_running.md
- Examples:
- Examples: examples/README.md
- gmx_MMPBSA_test: examples/gmx_MMPBSA_test.md
- Systems:
- Protein-protein: examples/Protein_protein/README.md
- Protein-ligand: examples/Protein_ligand/ST/README.md
- Protein-DNA: examples/Protein_DNA/README.md
- Protein-glycan: examples/Protein_glycan/README.md
- Membrane proteins: examples/Protein_membrane/README.md
- Metalloprotein-ligand: examples/Metalloprotein_ligand/README.md
- Multicomponent system: examples/Comp_receptor/README.md
- COVID-19 related proteins:
- Info: examples/COVID-19_related_proteins/README.md
- Main protease: examples/COVID-19_related_proteins/Main_protease_7l5d/README.md
- Papain-like protease: examples/COVID-19_related_proteins/Papain-like_protease_7koj/README.md
- S1-ACE2 complex: examples/COVID-19_related_proteins/S1-ACE2_complex_7dmu/README.md
- S1 RBD with antibody: examples/COVID-19_related_proteins/S1_RBD_with_antibody_6zlr/README.md
- CHARMMff Support:
- Protein-ligand: examples/Protein_ligand_CHARMMff/README.md
- Protein-ligand complex embedded in membrane: examples/Protein_membrane_CHARMMff/README.md
- Protein-ligand with LPH particles (ST): examples/Protein_ligand_LPH_atoms_CHARMMff/README.md
- OPLSff Support:
- Protein-protein: examples/OPLS/protein_protein/README.md
- Analysis:
- Single Trajectory Protocol: examples/Protein_ligand/ST/README.md
- Multiple Trajectory Protocol: examples/Protein_ligand/MT/README.md
- BFE calculations:
- BFE calculation with GB: examples/Protein_ligand/ST/README.md
- BFE calculation with GBNSR6: examples/GBNSR6/README.md
- BFE calculation with Linear PB: examples/Linear_PB_solver/README.md
- BFE calculation with NonLinear PB : examples/NonLinear_PB_solver/README.md
- BFE calculation with 3D-RISM: examples/3D-RISM/README.md
- Alanine scanning: examples/Alanine_scanning/README.md
- Decomposition analysis: examples/Decomposition_analysis/README.md
- Entropy calculations:
- Interaction Entropy: examples/Entropy_calculations/Interaction_Entropy/README.md
- nmode Entropy: examples/Entropy_calculations/nmode/README.md
- C2 Entropy calculations: examples/Entropy_calculations/C2_Entropy/README.md
- Stability calculations: examples/Stability/README.md
- QM/MMGBSA: examples/QM_MMGBSA/README.md
- Correlation: examples/Correlation/README.md
- Support for psf_dcd files:
- Protein-protein: examples/psf_dcd/protein_protein/README.md
- Protein-ligand: examples/psf_dcd/protein_ligand/README.md
- Multicomponent system: examples/psf_dcd/multicomponent_system/README.md
- Help:
- Help: Q&A/README.md
- Installation: Q&A/installation.md
- OS issues: Q&A/OS_issues.md
- Calculations: Q&A/calculations.md
- Info:
- Changelog: changelog.md
- Compatibility: compatibility.md
- Private Policy: private_policy.md
- Cite gmx_MMPBSA: cite_us.md
extra_css:
- assets/stylesheets/termynal.css
- assets/stylesheets/custom.css
extra_javascript:
- assets/js/termynal.js
- assets/js/custom.js