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Introduction to coarse graining: 2025 CCPBioSim Training Week

Authors: Robert Clark, Iain Peter Shand Smith

Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.

We have separated the content into 5 conceptually distinct parts:

  1. Construction of an AA membrane protein system
  2. Simulation/Visualisation of the AA system
  3. Construction of a CG membrane protein system
  4. Equilibration of the CG system
  5. Analysis of protein function and membrane dynamics

The user should work sequentially through each numbered directory within this repo
starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis

We acknowledge the work published by the Vanni lab which inspired the topic of this practical:

Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121

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Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025

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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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Introduction to coarse graining: 2025 CCPBioSim Training Week
Authors: Robert Clark, Iain Peter Shand Smith
Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.
We have separated the content into 5 conceptually distinct parts:
  1. Construction of an AA membrane protein system
  2. Simulation/Visualisation of the AA system
  3. Construction of a CG membrane protein system
  4. Equilibration of the CG system
  5. Analysis of protein function and membrane dynamics
The user should work sequentially through each numbered directory within this repo

starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis
We acknowledge the work published by the Vanni lab which inspired the topic of this practical:
Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121
About
Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025
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coarsecobydynamicsfunctiongraininginsertaselipidmartinizemembraneppm3proteinproteinsscramblasestructuretutorialyidc
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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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Introduction to coarse graining: 2025 CCPBioSim Training Week
Authors: Robert Clark, Iain Peter Shand Smith
Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.
We have separated the content into 5 conceptually distinct parts:
  1. Construction of an AA membrane protein system
  2. Simulation/Visualisation of the AA system
  3. Construction of a CG membrane protein system
  4. Equilibration of the CG system
  5. Analysis of protein function and membrane dynamics
The user should work sequentially through each numbered directory within this repo

starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis
We acknowledge the work published by the Vanni lab which inspired the topic of this practical:
Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121
About
Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025
Topics
coarsecobydynamicsfunctiongraininginsertaselipidmartinizemembraneppm3proteinproteinsscramblasestructuretutorialyidc
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Readme
GPL-3.0 license
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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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Introduction to coarse graining: 2025 CCPBioSim Training Week
Authors: Robert Clark, Iain Peter Shand Smith
Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.
We have separated the content into 5 conceptually distinct parts:
  1. Construction of an AA membrane protein system
  2. Simulation/Visualisation of the AA system
  3. Construction of a CG membrane protein system
  4. Equilibration of the CG system
  5. Analysis of protein function and membrane dynamics
The user should work sequentially through each numbered directory within this repo

starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis
We acknowledge the work published by the Vanni lab which inspired the topic of this practical:
Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121
About
Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025
Topics
coarsecobydynamicsfunctiongraininginsertaselipidmartinizemembraneppm3proteinproteinsscramblasestructuretutorialyidc
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Readme
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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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Introduction to coarse graining: 2025 CCPBioSim Training Week
Authors: Robert Clark, Iain Peter Shand Smith
Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.
We have separated the content into 5 conceptually distinct parts:
  1. Construction of an AA membrane protein system
  2. Simulation/Visualisation of the AA system
  3. Construction of a CG membrane protein system
  4. Equilibration of the CG system
  5. Analysis of protein function and membrane dynamics
The user should work sequentially through each numbered directory within this repo

starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis
We acknowledge the work published by the Vanni lab which inspired the topic of this practical:
Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121
About
Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025
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coarsecobydynamicsfunctiongraininginsertaselipidmartinizemembraneppm3proteinproteinsscramblasestructuretutorialyidc
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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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Introduction to coarse graining: 2025 CCPBioSim Training Week
Authors: Robert Clark, Iain Peter Shand Smith
Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.
We have separated the content into 5 conceptually distinct parts:
  1. Construction of an AA membrane protein system
  2. Simulation/Visualisation of the AA system
  3. Construction of a CG membrane protein system
  4. Equilibration of the CG system
  5. Analysis of protein function and membrane dynamics
The user should work sequentially through each numbered directory within this repo

starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis
We acknowledge the work published by the Vanni lab which inspired the topic of this practical:
Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121
About
Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025
Topics
coarsecobydynamicsfunctiongraininginsertaselipidmartinizemembraneppm3proteinproteinsscramblasestructuretutorialyidc
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Readme
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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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Introduction to coarse graining: 2025 CCPBioSim Training Week
Authors: Robert Clark, Iain Peter Shand Smith
Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.
We have separated the content into 5 conceptually distinct parts:
  1. Construction of an AA membrane protein system
  2. Simulation/Visualisation of the AA system
  3. Construction of a CG membrane protein system
  4. Equilibration of the CG system
  5. Analysis of protein function and membrane dynamics
The user should work sequentially through each numbered directory within this repo

starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis
We acknowledge the work published by the Vanni lab which inspired the topic of this practical:
Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121
About
Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025
Topics
coarsecobydynamicsfunctiongraininginsertaselipidmartinizemembraneppm3proteinproteinsscramblasestructuretutorialyidc
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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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Introduction to coarse graining: 2025 CCPBioSim Training Week
Authors: Robert Clark, Iain Peter Shand Smith
Here we present a practical introduction to the construction and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.
We have separated the content into 5 conceptually distinct parts:
  1. Construction of an AA membrane protein system
  2. Simulation/Visualisation of the AA system
  3. Construction of a CG membrane protein system
  4. Equilibration of the CG system
  5. Analysis of protein function and membrane dynamics
The user should work sequentially through each numbered directory within this repo

starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis
We acknowledge the work published by the Vanni lab which inspired the topic of this practical:
Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121
About
Introduction to Coarse Graining with YidC: CCPBioSim Training Week 2025
Topics
coarsecobydynamicsfunctiongraininginsertaselipidmartinizemembraneppm3proteinproteinsscramblasestructuretutorialyidc
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Readme
GPL-3.0 license
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