Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol #427

Open
#430
Open
Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol#427
#430
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amruthesht

Description

@amruthesht
amruthesht
opened on Jul 25, 2025

User story

As a user familiar with MDAnalysis, but unaware of the new IMDReader-IMDv3 feature, I would want to easily discover and learn how to use the streaming reader with the new IMDv3 protocol support without having to dig through API docs.

Additional context

MDAnalysis is adding (recently added) support for real-time streaming via the IMDv3 protocol through the new IMDReader, but this feature is only documented in the API docs. Most users read the UserGuide to learn about MDA capabilities, so they're unlikely to discover this functionality. The current API docs assumes that users already know about streaming and focuses on technical details rather than helping them understand what it is, and when and how to use it.

This creates a discoverability gap for a feature that could change how users approach simulation analysis - enabling real-time monitoring, and in-situ analysis.

Proposed UserGuide Documentation Structure

1. Introduction: What is streaming?

  • Brief explanation of IMDv3 protocol vs traditional file-based analysis
  • Benefits: real-time monitoring, in-situ analysis et al.

2. When to use streaming?

  • Real-time quality control and monitoring (Long-running simulations where early feedback is valuable)
  • Adaptive sampling, selection
  • Interactive visualization during simulation
  • Avoid large data storage - in-situ analysis

3. Installation and setup

  • Installing imdclient: pip install imdclient
  • MD engine support status and configuration:
    • GROMACS: example .mdp settings and mdrun flags
    • LAMMPS: configuration examples
    • NAMD: configuration examples
  • Links to engine-specific documentation

4. Basic streaming example - how to use IMDReader

Basic example using streaming, something like ---

importMDAnalysisasmda# Connect to running simulationu=mda.Universe("topol.tpr", "imd://localhost:8889")
# Streaming loopfortsinu.trajectory:
printstreaming_info# Your analysis code hereifsome_stopping_condition:
break

5. Additional features

Features that are available through IMDClient via the IMDReader

  • continue_after_disconnect
  • buffer_size
  • pause/resume? (not available directly)

6. Analysis workflows

  • Integration with MDAnalysis analysis modules
    (which analysis methods work/don't with IMDv3 MDA (limitations from StreamReaderBase)
  • Examples?

7. Complete working example

End-to-end workflow: GROMACS/NAMD/LAMMPS setup and streaming --> IMDReader --> visualization/analysis

8. Current limitations

  • Limitations with accessing data
    • implications for analysis usage
    • (from streamreaderbase)

Above information needs to be updated as imd.rst under doc/source/formats/reference

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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
    Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol #427
    Open
    #430
    Open
    Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol#427
    #430
    Assignees
    amruthesht
    Description
    @amruthesht
    amruthesht
    opened on Jul 25, 2025
    User story
    As a user familiar with MDAnalysis, but unaware of the new IMDReader-IMDv3 feature, I would want to easily discover and learn how to use the streaming reader with the new IMDv3 protocol support without having to dig through API docs.
    Additional context
    MDAnalysis is adding (recently added) support for real-time streaming via the IMDv3 protocol through the new IMDReader, but this feature is only documented in the API docs. Most users read the UserGuide to learn about MDA capabilities, so they're unlikely to discover this functionality. The current API docs assumes that users already know about streaming and focuses on technical details rather than helping them understand what it is, and when and how to use it.
    This creates a discoverability gap for a feature that could change how users approach simulation analysis - enabling real-time monitoring, and in-situ analysis.
    Proposed UserGuide Documentation Structure
    1. Introduction: What is streaming?
    • Brief explanation of IMDv3 protocol vs traditional file-based analysis
    • Benefits: real-time monitoring, in-situ analysis et al.
    2. When to use streaming?
    • Real-time quality control and monitoring (Long-running simulations where early feedback is valuable)
    • Adaptive sampling, selection
    • Interactive visualization during simulation
    • Avoid large data storage - in-situ analysis
    3. Installation and setup
    • Installing imdclient: pip install imdclient
    • MD engine support status and configuration:

      • GROMACS: example .mdp settings and mdrun flags
      • LAMMPS: configuration examples
      • NAMD: configuration examples
    • Links to engine-specific documentation
    4. Basic streaming example - how to use IMDReader
    Basic example using streaming, something like ---
    importMDAnalysisasmda# Connect to running simulationu=mda.Universe("topol.tpr", "imd://localhost:8889")
# Streaming loopfortsinu.trajectory:
printstreaming_info# Your analysis code hereifsome_stopping_condition:
break
    5. Additional features
    Features that are available through IMDClient via the IMDReader
    • continue_after_disconnect
    • buffer_size
    • pause/resume? (not available directly)
    6. Analysis workflows
    • Integration with MDAnalysis analysis modules
      
(which analysis methods work/don't with IMDv3 MDA (limitations from StreamReaderBase)
    • Examples?
    7. Complete working example
    End-to-end workflow: GROMACS/NAMD/LAMMPS setup and streaming --> IMDReader --> visualization/analysis
    8. Current limitations
    • Limitations with accessing data

      • implications for analysis usage
      • (from streamreaderbase)
    Above information needs to be updated as imd.rst under doc/source/formats/reference
    Activity
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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('^' + ".*" + '

      Skip to content
      Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol #427
      Open
      #430
      Open
      Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol#427
      #430
      Assignees
      amruthesht
      Description
      @amruthesht
      amruthesht
      opened on Jul 25, 2025
      User story
      As a user familiar with MDAnalysis, but unaware of the new IMDReader-IMDv3 feature, I would want to easily discover and learn how to use the streaming reader with the new IMDv3 protocol support without having to dig through API docs.
      Additional context
      MDAnalysis is adding (recently added) support for real-time streaming via the IMDv3 protocol through the new IMDReader, but this feature is only documented in the API docs. Most users read the UserGuide to learn about MDA capabilities, so they're unlikely to discover this functionality. The current API docs assumes that users already know about streaming and focuses on technical details rather than helping them understand what it is, and when and how to use it.
      This creates a discoverability gap for a feature that could change how users approach simulation analysis - enabling real-time monitoring, and in-situ analysis.
      Proposed UserGuide Documentation Structure
      1. Introduction: What is streaming?
      • Brief explanation of IMDv3 protocol vs traditional file-based analysis
      • Benefits: real-time monitoring, in-situ analysis et al.
      2. When to use streaming?
      • Real-time quality control and monitoring (Long-running simulations where early feedback is valuable)
      • Adaptive sampling, selection
      • Interactive visualization during simulation
      • Avoid large data storage - in-situ analysis
      3. Installation and setup
      • Installing imdclient: pip install imdclient
      • MD engine support status and configuration:

        • GROMACS: example .mdp settings and mdrun flags
        • LAMMPS: configuration examples
        • NAMD: configuration examples
      • Links to engine-specific documentation
      4. Basic streaming example - how to use IMDReader
      Basic example using streaming, something like ---
      importMDAnalysisasmda# Connect to running simulationu=mda.Universe("topol.tpr", "imd://localhost:8889")
# Streaming loopfortsinu.trajectory:
printstreaming_info# Your analysis code hereifsome_stopping_condition:
break
      5. Additional features
      Features that are available through IMDClient via the IMDReader
      • continue_after_disconnect
      • buffer_size
      • pause/resume? (not available directly)
      6. Analysis workflows
      • Integration with MDAnalysis analysis modules
        
(which analysis methods work/don't with IMDv3 MDA (limitations from StreamReaderBase)
      • Examples?
      7. Complete working example
      End-to-end workflow: GROMACS/NAMD/LAMMPS setup and streaming --> IMDReader --> visualization/analysis
      8. Current limitations
      • Limitations with accessing data

        • implications for analysis usage
        • (from streamreaderbase)
      Above information needs to be updated as imd.rst under doc/source/formats/reference
      Activity
      Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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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
        Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol #427
        Open
        #430
        Open
        Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol#427
        #430
        Assignees
        amruthesht
        Description
        @amruthesht
        amruthesht
        opened on Jul 25, 2025
        User story
        As a user familiar with MDAnalysis, but unaware of the new IMDReader-IMDv3 feature, I would want to easily discover and learn how to use the streaming reader with the new IMDv3 protocol support without having to dig through API docs.
        Additional context
        MDAnalysis is adding (recently added) support for real-time streaming via the IMDv3 protocol through the new IMDReader, but this feature is only documented in the API docs. Most users read the UserGuide to learn about MDA capabilities, so they're unlikely to discover this functionality. The current API docs assumes that users already know about streaming and focuses on technical details rather than helping them understand what it is, and when and how to use it.
        This creates a discoverability gap for a feature that could change how users approach simulation analysis - enabling real-time monitoring, and in-situ analysis.
        Proposed UserGuide Documentation Structure
        1. Introduction: What is streaming?
        • Brief explanation of IMDv3 protocol vs traditional file-based analysis
        • Benefits: real-time monitoring, in-situ analysis et al.
        2. When to use streaming?
        • Real-time quality control and monitoring (Long-running simulations where early feedback is valuable)
        • Adaptive sampling, selection
        • Interactive visualization during simulation
        • Avoid large data storage - in-situ analysis
        3. Installation and setup
        • Installing imdclient: pip install imdclient
        • MD engine support status and configuration:

          • GROMACS: example .mdp settings and mdrun flags
          • LAMMPS: configuration examples
          • NAMD: configuration examples
        • Links to engine-specific documentation
        4. Basic streaming example - how to use IMDReader
        Basic example using streaming, something like ---
        importMDAnalysisasmda# Connect to running simulationu=mda.Universe("topol.tpr", "imd://localhost:8889")
# Streaming loopfortsinu.trajectory:
printstreaming_info# Your analysis code hereifsome_stopping_condition:
break
        5. Additional features
        Features that are available through IMDClient via the IMDReader
        • continue_after_disconnect
        • buffer_size
        • pause/resume? (not available directly)
        6. Analysis workflows
        • Integration with MDAnalysis analysis modules
          
(which analysis methods work/don't with IMDv3 MDA (limitations from StreamReaderBase)
        • Examples?
        7. Complete working example
        End-to-end workflow: GROMACS/NAMD/LAMMPS setup and streaming --> IMDReader --> visualization/analysis
        8. Current limitations
        • Limitations with accessing data

          • implications for analysis usage
          • (from streamreaderbase)
        Above information needs to be updated as imd.rst under doc/source/formats/reference
        Activity
        Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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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
          Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol #427
          Open
          #430
          Open
          Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol#427
          #430
          Assignees
          amruthesht
          Description
          @amruthesht
          amruthesht
          opened on Jul 25, 2025
          User story
          As a user familiar with MDAnalysis, but unaware of the new IMDReader-IMDv3 feature, I would want to easily discover and learn how to use the streaming reader with the new IMDv3 protocol support without having to dig through API docs.
          Additional context
          MDAnalysis is adding (recently added) support for real-time streaming via the IMDv3 protocol through the new IMDReader, but this feature is only documented in the API docs. Most users read the UserGuide to learn about MDA capabilities, so they're unlikely to discover this functionality. The current API docs assumes that users already know about streaming and focuses on technical details rather than helping them understand what it is, and when and how to use it.
          This creates a discoverability gap for a feature that could change how users approach simulation analysis - enabling real-time monitoring, and in-situ analysis.
          Proposed UserGuide Documentation Structure
          1. Introduction: What is streaming?
          • Brief explanation of IMDv3 protocol vs traditional file-based analysis
          • Benefits: real-time monitoring, in-situ analysis et al.
          2. When to use streaming?
          • Real-time quality control and monitoring (Long-running simulations where early feedback is valuable)
          • Adaptive sampling, selection
          • Interactive visualization during simulation
          • Avoid large data storage - in-situ analysis
          3. Installation and setup
          • Installing imdclient: pip install imdclient
          • MD engine support status and configuration:

            • GROMACS: example .mdp settings and mdrun flags
            • LAMMPS: configuration examples
            • NAMD: configuration examples
          • Links to engine-specific documentation
          4. Basic streaming example - how to use IMDReader
          Basic example using streaming, something like ---
          importMDAnalysisasmda# Connect to running simulationu=mda.Universe("topol.tpr", "imd://localhost:8889")
# Streaming loopfortsinu.trajectory:
printstreaming_info# Your analysis code hereifsome_stopping_condition:
break
          5. Additional features
          Features that are available through IMDClient via the IMDReader
          • continue_after_disconnect
          • buffer_size
          • pause/resume? (not available directly)
          6. Analysis workflows
          • Integration with MDAnalysis analysis modules
            
(which analysis methods work/don't with IMDv3 MDA (limitations from StreamReaderBase)
          • Examples?
          7. Complete working example
          End-to-end workflow: GROMACS/NAMD/LAMMPS setup and streaming --> IMDReader --> visualization/analysis
          8. Current limitations
          • Limitations with accessing data

            • implications for analysis usage
            • (from streamreaderbase)
          Above information needs to be updated as imd.rst under doc/source/formats/reference
          Activity
          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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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('^' + ".*" + '

            Skip to content
            Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol #427
            Open
            #430
            Open
            Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol#427
            #430
            Assignees
            amruthesht
            Description
            @amruthesht
            amruthesht
            opened on Jul 25, 2025
            User story
            As a user familiar with MDAnalysis, but unaware of the new IMDReader-IMDv3 feature, I would want to easily discover and learn how to use the streaming reader with the new IMDv3 protocol support without having to dig through API docs.
            Additional context
            MDAnalysis is adding (recently added) support for real-time streaming via the IMDv3 protocol through the new IMDReader, but this feature is only documented in the API docs. Most users read the UserGuide to learn about MDA capabilities, so they're unlikely to discover this functionality. The current API docs assumes that users already know about streaming and focuses on technical details rather than helping them understand what it is, and when and how to use it.
            This creates a discoverability gap for a feature that could change how users approach simulation analysis - enabling real-time monitoring, and in-situ analysis.
            Proposed UserGuide Documentation Structure
            1. Introduction: What is streaming?
            • Brief explanation of IMDv3 protocol vs traditional file-based analysis
            • Benefits: real-time monitoring, in-situ analysis et al.
            2. When to use streaming?
            • Real-time quality control and monitoring (Long-running simulations where early feedback is valuable)
            • Adaptive sampling, selection
            • Interactive visualization during simulation
            • Avoid large data storage - in-situ analysis
            3. Installation and setup
            • Installing imdclient: pip install imdclient
            • MD engine support status and configuration:

              • GROMACS: example .mdp settings and mdrun flags
              • LAMMPS: configuration examples
              • NAMD: configuration examples
            • Links to engine-specific documentation
            4. Basic streaming example - how to use IMDReader
            Basic example using streaming, something like ---
            importMDAnalysisasmda# Connect to running simulationu=mda.Universe("topol.tpr", "imd://localhost:8889")
# Streaming loopfortsinu.trajectory:
printstreaming_info# Your analysis code hereifsome_stopping_condition:
break
            5. Additional features
            Features that are available through IMDClient via the IMDReader
            • continue_after_disconnect
            • buffer_size
            • pause/resume? (not available directly)
            6. Analysis workflows
            • Integration with MDAnalysis analysis modules
              
(which analysis methods work/don't with IMDv3 MDA (limitations from StreamReaderBase)
            • Examples?
            7. Complete working example
            End-to-end workflow: GROMACS/NAMD/LAMMPS setup and streaming --> IMDReader --> visualization/analysis
            8. Current limitations
            • Limitations with accessing data

              • implications for analysis usage
              • (from streamreaderbase)
            Above information needs to be updated as imd.rst under doc/source/formats/reference
            Activity
            Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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            Labels
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              No branches or pull requests
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, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

              Skip to content
              Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol #427
              Open
              #430
              Open
              Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol#427
              #430
              Assignees
              amruthesht
              Description
              @amruthesht
              amruthesht
              opened on Jul 25, 2025
              User story
              As a user familiar with MDAnalysis, but unaware of the new IMDReader-IMDv3 feature, I would want to easily discover and learn how to use the streaming reader with the new IMDv3 protocol support without having to dig through API docs.
              Additional context
              MDAnalysis is adding (recently added) support for real-time streaming via the IMDv3 protocol through the new IMDReader, but this feature is only documented in the API docs. Most users read the UserGuide to learn about MDA capabilities, so they're unlikely to discover this functionality. The current API docs assumes that users already know about streaming and focuses on technical details rather than helping them understand what it is, and when and how to use it.
              This creates a discoverability gap for a feature that could change how users approach simulation analysis - enabling real-time monitoring, and in-situ analysis.
              Proposed UserGuide Documentation Structure
              1. Introduction: What is streaming?
              • Brief explanation of IMDv3 protocol vs traditional file-based analysis
              • Benefits: real-time monitoring, in-situ analysis et al.
              2. When to use streaming?
              • Real-time quality control and monitoring (Long-running simulations where early feedback is valuable)
              • Adaptive sampling, selection
              • Interactive visualization during simulation
              • Avoid large data storage - in-situ analysis
              3. Installation and setup
              • Installing imdclient: pip install imdclient
              • MD engine support status and configuration:

                • GROMACS: example .mdp settings and mdrun flags
                • LAMMPS: configuration examples
                • NAMD: configuration examples
              • Links to engine-specific documentation
              4. Basic streaming example - how to use IMDReader
              Basic example using streaming, something like ---
              importMDAnalysisasmda# Connect to running simulationu=mda.Universe("topol.tpr", "imd://localhost:8889")
# Streaming loopfortsinu.trajectory:
printstreaming_info# Your analysis code hereifsome_stopping_condition:
break
              5. Additional features
              Features that are available through IMDClient via the IMDReader
              • continue_after_disconnect
              • buffer_size
              • pause/resume? (not available directly)
              6. Analysis workflows
              • Integration with MDAnalysis analysis modules
                
(which analysis methods work/don't with IMDv3 MDA (limitations from StreamReaderBase)
              • Examples?
              7. Complete working example
              End-to-end workflow: GROMACS/NAMD/LAMMPS setup and streaming --> IMDReader --> visualization/analysis
              8. Current limitations
              • Limitations with accessing data

                • implications for analysis usage
                • (from streamreaderbase)
              Above information needs to be updated as imd.rst under doc/source/formats/reference
              Activity
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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
                Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol #427
                Open
                #430
                Open
                Add UserGuide documentation for IMDReader - reading streaming data with IMDv3 protocol#427
                #430
                Assignees
                amruthesht
                Description
                @amruthesht
                amruthesht
                opened on Jul 25, 2025
                User story
                As a user familiar with MDAnalysis, but unaware of the new IMDReader-IMDv3 feature, I would want to easily discover and learn how to use the streaming reader with the new IMDv3 protocol support without having to dig through API docs.
                Additional context
                MDAnalysis is adding (recently added) support for real-time streaming via the IMDv3 protocol through the new IMDReader, but this feature is only documented in the API docs. Most users read the UserGuide to learn about MDA capabilities, so they're unlikely to discover this functionality. The current API docs assumes that users already know about streaming and focuses on technical details rather than helping them understand what it is, and when and how to use it.
                This creates a discoverability gap for a feature that could change how users approach simulation analysis - enabling real-time monitoring, and in-situ analysis.
                Proposed UserGuide Documentation Structure
                1. Introduction: What is streaming?
                • Brief explanation of IMDv3 protocol vs traditional file-based analysis
                • Benefits: real-time monitoring, in-situ analysis et al.
                2. When to use streaming?
                • Real-time quality control and monitoring (Long-running simulations where early feedback is valuable)
                • Adaptive sampling, selection
                • Interactive visualization during simulation
                • Avoid large data storage - in-situ analysis
                3. Installation and setup
                • Installing imdclient: pip install imdclient
                • MD engine support status and configuration:

                  • GROMACS: example .mdp settings and mdrun flags
                  • LAMMPS: configuration examples
                  • NAMD: configuration examples
                • Links to engine-specific documentation
                4. Basic streaming example - how to use IMDReader
                Basic example using streaming, something like ---
                importMDAnalysisasmda# Connect to running simulationu=mda.Universe("topol.tpr", "imd://localhost:8889")
# Streaming loopfortsinu.trajectory:
printstreaming_info# Your analysis code hereifsome_stopping_condition:
break
                5. Additional features
                Features that are available through IMDClient via the IMDReader
                • continue_after_disconnect
                • buffer_size
                • pause/resume? (not available directly)
                6. Analysis workflows
                • Integration with MDAnalysis analysis modules
                  
(which analysis methods work/don't with IMDv3 MDA (limitations from StreamReaderBase)
                • Examples?
                7. Complete working example
                End-to-end workflow: GROMACS/NAMD/LAMMPS setup and streaming --> IMDReader --> visualization/analysis
                8. Current limitations
                • Limitations with accessing data

                  • implications for analysis usage
                  • (from streamreaderbase)
                Above information needs to be updated as imd.rst under doc/source/formats/reference
                Activity
                Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                Metadata
                Metadata
                Assignees
                Labels
                No labels
                No labels
                Type
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                  Issue actions