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FESetup [Deprecated]

This code is no longer being developed or maintained.

FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields.

The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together.

FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged!

The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler (STFC) with contributions from the original developers.

Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup.

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A tool for setting up free energy simulations.

www.ccpbiosim.ac.uk/software

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obsoletesoftware

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37 stars

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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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FESetup [Deprecated]
This code is no longer being developed or maintained.
FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields.
The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together.
FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged!
The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler (STFC) with contributions from the original developers.
Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup.
About
A tool for setting up free energy simulations.
www.ccpbiosim.ac.uk/software
Topics
obsoletesoftware
Resources
Readme
GPL-2.0 license
Activity
Custom properties
Stars
37 stars
Watchers
4 watching
Forks
18 forks
Report repository
Releases
Packages
Contributors
Languages

, '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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FESetup [Deprecated]
This code is no longer being developed or maintained.
FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields.
The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together.
FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged!
The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler (STFC) with contributions from the original developers.
Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup.
About
A tool for setting up free energy simulations.
www.ccpbiosim.ac.uk/software
Topics
obsoletesoftware
Resources
Readme
GPL-2.0 license
Activity
Custom properties
Stars
37 stars
Watchers
4 watching
Forks
18 forks
Report repository
Releases
Packages
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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This repository was archived by the owner on Oct 16, 2025. It is now read-only.

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FESetup [Deprecated]
This code is no longer being developed or maintained.
FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields.
The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together.
FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged!
The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler (STFC) with contributions from the original developers.
Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup.
About
A tool for setting up free energy simulations.
www.ccpbiosim.ac.uk/software
Topics
obsoletesoftware
Resources
Readme
GPL-2.0 license
Activity
Custom properties
Stars
37 stars
Watchers
4 watching
Forks
18 forks
Report repository
Releases
Packages
Contributors
Languages

, '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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FESetup [Deprecated]
This code is no longer being developed or maintained.
FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields.
The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together.
FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged!
The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler (STFC) with contributions from the original developers.
Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup.
About
A tool for setting up free energy simulations.
www.ccpbiosim.ac.uk/software
Topics
obsoletesoftware
Resources
Readme
GPL-2.0 license
Activity
Custom properties
Stars
37 stars
Watchers
4 watching
Forks
18 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('^' + ".*" + '

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This repository was archived by the owner on Oct 16, 2025. It is now read-only.

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FESetup [Deprecated]
This code is no longer being developed or maintained.
FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields.
The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together.
FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged!
The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler (STFC) with contributions from the original developers.
Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup.
About
A tool for setting up free energy simulations.
www.ccpbiosim.ac.uk/software
Topics
obsoletesoftware
Resources
Readme
GPL-2.0 license
Activity
Custom properties
Stars
37 stars
Watchers
4 watching
Forks
18 forks
Report repository
Releases
Packages
Contributors
Languages

, '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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This repository was archived by the owner on Oct 16, 2025. It is now read-only.

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FESetup [Deprecated]
This code is no longer being developed or maintained.
FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields.
The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together.
FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged!
The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler (STFC) with contributions from the original developers.
Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup.
About
A tool for setting up free energy simulations.
www.ccpbiosim.ac.uk/software
Topics
obsoletesoftware
Resources
Readme
GPL-2.0 license
Activity
Custom properties
Stars
37 stars
Watchers
4 watching
Forks
18 forks
Report repository
Releases
Packages
Contributors
Languages

, '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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FESetup [Deprecated]
This code is no longer being developed or maintained.
FESetup automates the setup of relative alchemical free energy (AFE) simulations such as thermodynamic integration (TI) and free energy perturbation (FEP). Post–processing methods like MM–PBSA and LIE are supported as well. FESetup can also be used for general simulation setup ("equilibration") through an abstract MD engine (currently supported MD engines are AMBER, GROMACS, NAMD and DL_POLY). For relative AFE simulation the mapping of corresponding atoms between the two free energy states, that is their topological similarity, is computed via a maximum common substructure search (MCSS). This enables a maximal single topology description of the perturbed molecule pair. Ligand molecules can automatically be parameterised using the AMBER GAFF/AM1-BCC method. Supported force fields for biomolecules are all the modern AMBER force fields.
The AFE simulation packages that are currently supported are Sire, AMBER, GROMACS and CHARMM/PERT. All these codes implement AFE simulation by making use of a hybrid single/dual topology description of the perturbed region i.e. the mapped region (single topology) can be used simultaneously with an un–mapped, duplicated region (dual topology) from each state. There is also some support for NAMD's purely dual topology implementation but this requires an additional PDB file to mark appearing/vanishing atoms and possibly relative restraints to keep ligands spatially in place and/or together.
FESetup particularly aims at automation where it makes sense and is possible, ease of use and robustness of the code. Users are very welcome to discuss on our forum, report issues and request new features. The software is licensed under the GPL2 and such is a community effort: user contributions in any form are highly encouraged!
The basis of the current code was a collection of Python and shell scripts written previously by Julien Michel and Christopher Woods. The current code base is now mainly developed by Hannes Loeffler (STFC) with contributions from the original developers.
Please cite DOI: 10.1021/acs.jcim.5b00368 when you use FESetup.
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A tool for setting up free energy simulations.
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