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MDAnalysis Repository README

Build StatusCoverage Status[*]

Documentation (latest release)Documentation (development version)User Google GroupDeveloper Google GroupAnacondaMy Binder

MDAnalysis is a Python toolkit to analyze molecular dynamics trajectories generated by a wide range of popular simulation packages including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the lists of supported trajectory formats and topology formats.)

importMDAnalysisasmda# Load simulation results with a single lineu=mda.Universe('topol.tpr','traj.trr')
# Select atomsag=u.select_atoms('name OH')
# Atom data made available as Numpy arraysag.positionsag.velocitiesag.forces# Iterate through trajectoriesfortsinu.trajectory:
print(ag.center_of_mass())

There are also a number of tutorials on the MDAnalysis homepage that explain how to conduct RMSD calculations, Alignment and more features of MDAnalysis.

Source code

Source code is hosted in a git repository at

https://github.com/MDAnalysis/mdanalysis

and is available under the GNU General Public License, version 2 (see the file LICENSE).

This is the top level of the master repository. It contains

  1. the MDAnalysis toolkit source files in the directory

    package/

  2. the unit tests together with any input files required for running those tests in the directory

    testsuite/

The directory maintainer contains scripts only needed for maintaining releases and are not generally useful for the user or the typical developer.

(For more details on the directory layout see Issue 87 on the MDAnalysis issue tracker.)

Guide for Developers

To setup a development environment and run the testsuite you can use this guide. If you are a new developer who would like to start contributing to MDAnalysis as a start you can increase our code coverage, the guides explain how to find uncovered code.

[*]build: Unit testing is for the whole package; coverage is shown for the core library modules and the analysis modules.

About

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mdanalysis.org

Resources

Readme
License

Code of conduct

Code of conduct

Contributing

Contributing
Activity

Stars

0 stars

Watchers

0 watching

Forks

0 forks
Report repository

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
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MDAnalysis Repository README
Build StatusCoverage Status[*]
Documentation (latest release)Documentation (development version)User Google GroupDeveloper Google GroupAnacondaMy Binder
MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation packages
including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the
lists of supported trajectory formats and topology formats.)
importMDAnalysisasmda# Load simulation results with a single lineu=mda.Universe('topol.tpr','traj.trr')
# Select atomsag=u.select_atoms('name OH')
# Atom data made available as Numpy arraysag.positionsag.velocitiesag.forces# Iterate through trajectoriesfortsinu.trajectory:
print(ag.center_of_mass())
There are also a number of tutorials on the MDAnalysis homepage that explain
how to conduct RMSD calculations, Alignment and more features of MDAnalysis.
Source code
Source code is hosted in a git repository at
https://github.com/MDAnalysis/mdanalysis
and is available under the GNU General Public License, version 2 (see
the file LICENSE).
This is the top level of the master repository. It contains
  1. the MDAnalysis toolkit source files in the directory
    package/

  2. the unit tests together with any input files required for
running those tests in the directory
    testsuite/

The directory maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
typical developer.
(For more details on the directory layout see Issue 87 on the
MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this
guide. If you are a new developer who would like to start contributing to
MDAnalysis as a start you can increase our code coverage, the guides explain how
to find uncovered code.
[*]build: Unit testing is for the whole package; coverage is
shown for the core library modules and the analysis modules.
About
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
mdanalysis.org
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
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0 forks
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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");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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MDAnalysis Repository README
Build StatusCoverage Status[*]
Documentation (latest release)Documentation (development version)User Google GroupDeveloper Google GroupAnacondaMy Binder
MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation packages
including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the
lists of supported trajectory formats and topology formats.)
importMDAnalysisasmda# Load simulation results with a single lineu=mda.Universe('topol.tpr','traj.trr')
# Select atomsag=u.select_atoms('name OH')
# Atom data made available as Numpy arraysag.positionsag.velocitiesag.forces# Iterate through trajectoriesfortsinu.trajectory:
print(ag.center_of_mass())
There are also a number of tutorials on the MDAnalysis homepage that explain
how to conduct RMSD calculations, Alignment and more features of MDAnalysis.
Source code
Source code is hosted in a git repository at
https://github.com/MDAnalysis/mdanalysis
and is available under the GNU General Public License, version 2 (see
the file LICENSE).
This is the top level of the master repository. It contains
  1. the MDAnalysis toolkit source files in the directory
    package/

  2. the unit tests together with any input files required for
running those tests in the directory
    testsuite/

The directory maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
typical developer.
(For more details on the directory layout see Issue 87 on the
MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this
guide. If you are a new developer who would like to start contributing to
MDAnalysis as a start you can increase our code coverage, the guides explain how
to find uncovered code.
[*]build: Unit testing is for the whole package; coverage is
shown for the core library modules and the analysis modules.
About
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
mdanalysis.org
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
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, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
MDAnalysis Repository README
Build StatusCoverage Status[*]
Documentation (latest release)Documentation (development version)User Google GroupDeveloper Google GroupAnacondaMy Binder
MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation packages
including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the
lists of supported trajectory formats and topology formats.)
importMDAnalysisasmda# Load simulation results with a single lineu=mda.Universe('topol.tpr','traj.trr')
# Select atomsag=u.select_atoms('name OH')
# Atom data made available as Numpy arraysag.positionsag.velocitiesag.forces# Iterate through trajectoriesfortsinu.trajectory:
print(ag.center_of_mass())
There are also a number of tutorials on the MDAnalysis homepage that explain
how to conduct RMSD calculations, Alignment and more features of MDAnalysis.
Source code
Source code is hosted in a git repository at
https://github.com/MDAnalysis/mdanalysis
and is available under the GNU General Public License, version 2 (see
the file LICENSE).
This is the top level of the master repository. It contains
  1. the MDAnalysis toolkit source files in the directory
    package/

  2. the unit tests together with any input files required for
running those tests in the directory
    testsuite/

The directory maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
typical developer.
(For more details on the directory layout see Issue 87 on the
MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this
guide. If you are a new developer who would like to start contributing to
MDAnalysis as a start you can increase our code coverage, the guides explain how
to find uncovered code.
[*]build: Unit testing is for the whole package; coverage is
shown for the core library modules and the analysis modules.
About
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
mdanalysis.org
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
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Contributors
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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" + '

Skip to content
BranchesTags
Repository files navigation
MDAnalysis Repository README
Build StatusCoverage Status[*]
Documentation (latest release)Documentation (development version)User Google GroupDeveloper Google GroupAnacondaMy Binder
MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation packages
including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the
lists of supported trajectory formats and topology formats.)
importMDAnalysisasmda# Load simulation results with a single lineu=mda.Universe('topol.tpr','traj.trr')
# Select atomsag=u.select_atoms('name OH')
# Atom data made available as Numpy arraysag.positionsag.velocitiesag.forces# Iterate through trajectoriesfortsinu.trajectory:
print(ag.center_of_mass())
There are also a number of tutorials on the MDAnalysis homepage that explain
how to conduct RMSD calculations, Alignment and more features of MDAnalysis.
Source code
Source code is hosted in a git repository at
https://github.com/MDAnalysis/mdanalysis
and is available under the GNU General Public License, version 2 (see
the file LICENSE).
This is the top level of the master repository. It contains
  1. the MDAnalysis toolkit source files in the directory
    package/

  2. the unit tests together with any input files required for
running those tests in the directory
    testsuite/

The directory maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
typical developer.
(For more details on the directory layout see Issue 87 on the
MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this
guide. If you are a new developer who would like to start contributing to
MDAnalysis as a start you can increase our code coverage, the guides explain how
to find uncovered code.
[*]build: Unit testing is for the whole package; coverage is
shown for the core library modules and the analysis modules.
About
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
mdanalysis.org
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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
BranchesTags
Repository files navigation
MDAnalysis Repository README
Build StatusCoverage Status[*]
Documentation (latest release)Documentation (development version)User Google GroupDeveloper Google GroupAnacondaMy Binder
MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation packages
including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the
lists of supported trajectory formats and topology formats.)
importMDAnalysisasmda# Load simulation results with a single lineu=mda.Universe('topol.tpr','traj.trr')
# Select atomsag=u.select_atoms('name OH')
# Atom data made available as Numpy arraysag.positionsag.velocitiesag.forces# Iterate through trajectoriesfortsinu.trajectory:
print(ag.center_of_mass())
There are also a number of tutorials on the MDAnalysis homepage that explain
how to conduct RMSD calculations, Alignment and more features of MDAnalysis.
Source code
Source code is hosted in a git repository at
https://github.com/MDAnalysis/mdanalysis
and is available under the GNU General Public License, version 2 (see
the file LICENSE).
This is the top level of the master repository. It contains
  1. the MDAnalysis toolkit source files in the directory
    package/

  2. the unit tests together with any input files required for
running those tests in the directory
    testsuite/

The directory maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
typical developer.
(For more details on the directory layout see Issue 87 on the
MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this
guide. If you are a new developer who would like to start contributing to
MDAnalysis as a start you can increase our code coverage, the guides explain how
to find uncovered code.
[*]build: Unit testing is for the whole package; coverage is
shown for the core library modules and the analysis modules.
About
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
mdanalysis.org
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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
BranchesTags
Repository files navigation
MDAnalysis Repository README
Build StatusCoverage Status[*]
Documentation (latest release)Documentation (development version)User Google GroupDeveloper Google GroupAnacondaMy Binder
MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation packages
including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the
lists of supported trajectory formats and topology formats.)
importMDAnalysisasmda# Load simulation results with a single lineu=mda.Universe('topol.tpr','traj.trr')
# Select atomsag=u.select_atoms('name OH')
# Atom data made available as Numpy arraysag.positionsag.velocitiesag.forces# Iterate through trajectoriesfortsinu.trajectory:
print(ag.center_of_mass())
There are also a number of tutorials on the MDAnalysis homepage that explain
how to conduct RMSD calculations, Alignment and more features of MDAnalysis.
Source code
Source code is hosted in a git repository at
https://github.com/MDAnalysis/mdanalysis
and is available under the GNU General Public License, version 2 (see
the file LICENSE).
This is the top level of the master repository. It contains
  1. the MDAnalysis toolkit source files in the directory
    package/

  2. the unit tests together with any input files required for
running those tests in the directory
    testsuite/

The directory maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
typical developer.
(For more details on the directory layout see Issue 87 on the
MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this
guide. If you are a new developer who would like to start contributing to
MDAnalysis as a start you can increase our code coverage, the guides explain how
to find uncovered code.
[*]build: Unit testing is for the whole package; coverage is
shown for the core library modules and the analysis modules.
About
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
mdanalysis.org
Resources
Readme
License
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
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); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
MDAnalysis Repository README
Build StatusCoverage Status[*]
Documentation (latest release)Documentation (development version)User Google GroupDeveloper Google GroupAnacondaMy Binder
MDAnalysis is a Python toolkit to analyze molecular dynamics
trajectories generated by a wide range of popular simulation packages
including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the
lists of supported trajectory formats and topology formats.)
importMDAnalysisasmda# Load simulation results with a single lineu=mda.Universe('topol.tpr','traj.trr')
# Select atomsag=u.select_atoms('name OH')
# Atom data made available as Numpy arraysag.positionsag.velocitiesag.forces# Iterate through trajectoriesfortsinu.trajectory:
print(ag.center_of_mass())
There are also a number of tutorials on the MDAnalysis homepage that explain
how to conduct RMSD calculations, Alignment and more features of MDAnalysis.
Source code
Source code is hosted in a git repository at
https://github.com/MDAnalysis/mdanalysis
and is available under the GNU General Public License, version 2 (see
the file LICENSE).
This is the top level of the master repository. It contains
  1. the MDAnalysis toolkit source files in the directory
    package/

  2. the unit tests together with any input files required for
running those tests in the directory
    testsuite/

The directory maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
typical developer.
(For more details on the directory layout see Issue 87 on the
MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this
guide. If you are a new developer who would like to start contributing to
MDAnalysis as a start you can increase our code coverage, the guides explain how
to find uncovered code.
[*]build: Unit testing is for the whole package; coverage is
shown for the core library modules and the analysis modules.
About
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
mdanalysis.org
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