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MDAnalysis User Guide

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MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.

This repository contains the user guide for MDAnalysis. The user guide originated as a project for Google Season of Docs 2019-2020.

The code in the user guide is released under the GNU LGPL v2.1+ license, while text and images are released under the CC BY-SA 4.0 DEED license.

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User Guide for MDAnalysis

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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MDAnalysis User Guide
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MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
This repository contains the user guide for MDAnalysis. The user guide originated as a project for Google Season of Docs 2019-2020.
The code in the user guide is released under the GNU LGPL v2.1+ license, while text and images are released under the CC BY-SA 4.0 DEED license.
About
User Guide for MDAnalysis
userguide.mdanalysis.org
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
31 stars
Watchers
10 watching
Forks
49 forks
Report repository
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Used by
Contributors
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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MDAnalysis User Guide
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User Google GroupDeveloper Google Group
MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
This repository contains the user guide for MDAnalysis. The user guide originated as a project for Google Season of Docs 2019-2020.
The code in the user guide is released under the GNU LGPL v2.1+ license, while text and images are released under the CC BY-SA 4.0 DEED license.
About
User Guide for MDAnalysis
userguide.mdanalysis.org
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
31 stars
Watchers
10 watching
Forks
49 forks
Report repository
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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MDAnalysis User Guide
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MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
This repository contains the user guide for MDAnalysis. The user guide originated as a project for Google Season of Docs 2019-2020.
The code in the user guide is released under the GNU LGPL v2.1+ license, while text and images are released under the CC BY-SA 4.0 DEED license.
About
User Guide for MDAnalysis
userguide.mdanalysis.org
Resources
Readme
LGPL-2.1 license
Activity
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Stars
31 stars
Watchers
10 watching
Forks
49 forks
Report repository
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Used by
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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MDAnalysis User Guide
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User Google GroupDeveloper Google Group
MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
This repository contains the user guide for MDAnalysis. The user guide originated as a project for Google Season of Docs 2019-2020.
The code in the user guide is released under the GNU LGPL v2.1+ license, while text and images are released under the CC BY-SA 4.0 DEED license.
About
User Guide for MDAnalysis
userguide.mdanalysis.org
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
31 stars
Watchers
10 watching
Forks
49 forks
Report repository
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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MDAnalysis User Guide
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User Google GroupDeveloper Google Group
MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
This repository contains the user guide for MDAnalysis. The user guide originated as a project for Google Season of Docs 2019-2020.
The code in the user guide is released under the GNU LGPL v2.1+ license, while text and images are released under the CC BY-SA 4.0 DEED license.
About
User Guide for MDAnalysis
userguide.mdanalysis.org
Resources
Readme
LGPL-2.1 license
Activity
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Stars
31 stars
Watchers
10 watching
Forks
49 forks
Report repository
Packages
Used by
Contributors
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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MDAnalysis User Guide
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User Google GroupDeveloper Google Group
MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
This repository contains the user guide for MDAnalysis. The user guide originated as a project for Google Season of Docs 2019-2020.
The code in the user guide is released under the GNU LGPL v2.1+ license, while text and images are released under the CC BY-SA 4.0 DEED license.
About
User Guide for MDAnalysis
userguide.mdanalysis.org
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
31 stars
Watchers
10 watching
Forks
49 forks
Report repository
Packages
Used by
Contributors
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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MDAnalysis User Guide
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User Google GroupDeveloper Google Group
MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in many popular formats. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
This repository contains the user guide for MDAnalysis. The user guide originated as a project for Google Season of Docs 2019-2020.
The code in the user guide is released under the GNU LGPL v2.1+ license, while text and images are released under the CC BY-SA 4.0 DEED license.
About
User Guide for MDAnalysis
userguide.mdanalysis.org
Resources
Readme
LGPL-2.1 license
Activity
Custom properties
Stars
31 stars
Watchers
10 watching
Forks
49 forks
Report repository
Packages
Used by
Contributors
Languages