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PyMD-Notebook

PythonLicenseJupyter

PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).

Key Features

Molecular Dynamics Simulation

  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).

Output Analysis

  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.

Python Compatibility

  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.

Usage

  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.

License

This repository is licensed under the MIT License.

About

Simple Jupyter notebook for performing classical Molecular Dynamics simulations, including analysis of final atomic configurations and radial distribution functions (RDF).

Topics

atomic-simulationjupyter-notebookmolecular-dynamicsmolecular-dynamics-simulationpython3radial-distribution-functionsimulation

Resources

Readme
MIT license
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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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PyMD-Notebook
PythonLicenseJupyter
PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).
Key Features
Molecular Dynamics Simulation
  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).
Output Analysis
  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.
Python Compatibility
  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.
Usage
  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.
License
This repository is licensed under the MIT License.
About
Simple Jupyter notebook for performing classical Molecular Dynamics simulations, including analysis of final atomic configurations and radial distribution functions (RDF).
Topics
atomic-simulationjupyter-notebookmolecular-dynamicsmolecular-dynamics-simulationpython3radial-distribution-functionsimulation
Resources
Readme
MIT license
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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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PyMD-Notebook
PythonLicenseJupyter
PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).
Key Features
Molecular Dynamics Simulation
  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).
Output Analysis
  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.
Python Compatibility
  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.
Usage
  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.
License
This repository is licensed under the MIT License.
About
Simple Jupyter notebook for performing classical Molecular Dynamics simulations, including analysis of final atomic configurations and radial distribution functions (RDF).
Topics
atomic-simulationjupyter-notebookmolecular-dynamicsmolecular-dynamics-simulationpython3radial-distribution-functionsimulation
Resources
Readme
MIT license
Activity
Stars
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Watchers
0 watching
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0 forks
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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('^' + ".*" + '

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Repository files navigation
PyMD-Notebook
PythonLicenseJupyter
PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).
Key Features
Molecular Dynamics Simulation
  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).
Output Analysis
  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.
Python Compatibility
  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.
Usage
  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.
License
This repository is licensed under the MIT License.
About
Simple Jupyter notebook for performing classical Molecular Dynamics simulations, including analysis of final atomic configurations and radial distribution functions (RDF).
Topics
atomic-simulationjupyter-notebookmolecular-dynamicsmolecular-dynamics-simulationpython3radial-distribution-functionsimulation
Resources
Readme
MIT license
Activity
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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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Repository files navigation
PyMD-Notebook
PythonLicenseJupyter
PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).
Key Features
Molecular Dynamics Simulation
  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).
Output Analysis
  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.
Python Compatibility
  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.
Usage
  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.
License
This repository is licensed under the MIT License.
About
Simple Jupyter notebook for performing classical Molecular Dynamics simulations, including analysis of final atomic configurations and radial distribution functions (RDF).
Topics
atomic-simulationjupyter-notebookmolecular-dynamicsmolecular-dynamics-simulationpython3radial-distribution-functionsimulation
Resources
Readme
MIT license
Activity
Stars
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0 watching
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0 forks
Report repository
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, '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('^' + ".*" + '

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PyMD-Notebook
PythonLicenseJupyter
PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).
Key Features
Molecular Dynamics Simulation
  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).
Output Analysis
  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.
Python Compatibility
  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.
Usage
  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.
License
This repository is licensed under the MIT License.
About
Simple Jupyter notebook for performing classical Molecular Dynamics simulations, including analysis of final atomic configurations and radial distribution functions (RDF).
Topics
atomic-simulationjupyter-notebookmolecular-dynamicsmolecular-dynamics-simulationpython3radial-distribution-functionsimulation
Resources
Readme
MIT license
Activity
Stars
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Report repository
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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('^' + ".*" + '

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PyMD-Notebook
PythonLicenseJupyter
PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).
Key Features
Molecular Dynamics Simulation
  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).
Output Analysis
  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.
Python Compatibility
  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.
Usage
  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.
License
This repository is licensed under the MIT License.
About
Simple Jupyter notebook for performing classical Molecular Dynamics simulations, including analysis of final atomic configurations and radial distribution functions (RDF).
Topics
atomic-simulationjupyter-notebookmolecular-dynamicsmolecular-dynamics-simulationpython3radial-distribution-functionsimulation
Resources
Readme
MIT license
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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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PyMD-Notebook
PythonLicenseJupyter
PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).
Key Features
Molecular Dynamics Simulation
  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).
Output Analysis
  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.
Python Compatibility
  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.
Usage
  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.
License
This repository is licensed under the MIT License.
About
Simple Jupyter notebook for performing classical Molecular Dynamics simulations, including analysis of final atomic configurations and radial distribution functions (RDF).
Topics
atomic-simulationjupyter-notebookmolecular-dynamicsmolecular-dynamics-simulationpython3radial-distribution-functionsimulation
Resources
Readme
MIT license
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