L1 ⚛ L1-299 ⊙ Testnet

Classical Molecular Dynamics

Computational Chemistry · Empirical force-field dynamics

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⬇ L1-299.md

# ⚛ L1 Principle — Classical Molecular Dynamics **ID:** `L1-299` · **Status:** ⊙ Testnet (genesis catalog) > **🌐 Domain:** Computational Chemistry — *Empirical force-field dynamics* > **🎯 Problem class:** nonlinear inverse · **🧮 Solution space:** atomic trajectory > **📡 Carrier:** none · **🌫 Noise:** thermal langevin > **⚖ Difficulty (δ):** 3 · **⛓ Block:** 41554113 --- ## 🧠 1. Introduction **Classical Molecular Dynamics** is a **nonlinear inverse problem** whose unknown lives in **atomic trajectory** space, within the **Empirical force-field dynamics** sub-domain of **Computational Chemistry**. Measurements consist of none via a **md observable** sensing mechanism. The forward operator applies, in order: E · force field operator; D · time · symplectic operator; O · trajectory operator. Observations are corrupted by Langevin-type thermal fluctuations. Well-posed forward; force field validity limits accuracy. ## ⚙ 2. Forward Model Physical chain: **x** → E · force field → D · time · symplectic → O · trajectory → **y** (detector). ``` y = `O.trajectory` `D.time.symplectic` `E.force_field` x ``` **Measurement DAG:** | Primitive | What it does | |---|---| | `E.force_field` | E · force field operator | | `D.time.symplectic` | D · time · symplectic operator | | `O.trajectory` | O · trajectory operator | ## 🔬 3. Physics Fingerprint | Property | Value | |---|---| | Domain | Computational Chemistry | | Sub domain | Empirical force-field dynamics | | Carrier | none | | Problem class | nonlinear_inverse | | Solution space | atomic_trajectory | | Noise model | thermal_langevin | | Integration axis | time | | Difficulty delta | 3 | | L dag | 3 | ## 📡 4. Measurement Model Well-posed forward; force field validity limits accuracy. | Metric | Value | |---|---| | Metric | diffusion_coeff_relative_error | | Secondary | rdf_L2 | ## 📏 5. Operating Range (Ω) **Center problem class:** `classical_md` · **Forward operator:** `classical_md_forward` **Center point:** | Parameter | Unit | Value | |---|---|---| | Ff | — | AMBER | | T k | — | 300 | | Dt fs | — | 2 | | N atoms | — | 1000 | | N steps | — | 1e+06 | **Allowed bounds:** | Parameter | Unit | Range | |---|---|---| | Ff | — | AMBER, CHARMM, OPLS, GROMOS, ReaxFF | | T k | — | 4 – 5000 | | Dt fs | — | 0.1 – 10 | | N atoms | — | 100 – 10000000.0 | | N steps | — | 1000 – 10000000000.0 | ## 🎯 6. Tolerance (ε) **Center tolerance:** D rel error <= 0.04 | Metric | Range | |---|---| | Diffusion coeff relative error | 0.01 – 0.4 | ## ⚖ 7. Hardness Function Hardness scales as **`epsilon_fn`** on **diffusion_coeff_relative_error**, with κ = `200` and δ = `3`. ## 💾 8. Reference Dataset - **primary** · weight 1.0 · IPFS _(not pinned yet)_ ## 9. On-chain Registration - **Chain hash:** `0x6f7a21f466265980a27ed5c336113f7c954b12f77bc1ec83b1e322cf9cc1cca7` - **Chain tx hash:** `0xedfe0d821020fa241389cac3b3f6473eb5bdec18d03851ec5e90b623d512f436` - **Chain block:** `41554113` --- ## File Mapping This bundle consists of: `L1-299.md`, `L1-299.json`. | File | Role | How to regenerate | |------|------|-------------------| | `L1-299.md` | Source of truth — edit this | Human or LLM | | `L1-299.json` | Structured metadata for the registry | LLM regenerates from the sections above | **Prompt for your LLM after editing this Markdown:** > Read the attached Markdown. Regenerate the sibling `.json` so every field matches. > Preserve the schema documented in the rows above. > Output each file in its own fenced code block tagged with the filename. > Output only the JSON object. _This Markdown was auto-synthesized from the catalog row for `L1-299`._ _Edit it, regenerate the JSON, and submit at [/submit](/submit) to claim the artifact._

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Read the attached Markdown (L1-299.md).
Regenerate L1-299.json so every field matches the Markdown.
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L2-299-001 Classical Molecular Dynamics Mismatch-Only Spec

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📋 JSON metadata

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  "chain_block": 41554113,
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  "chain_tx_hash": "0xedfe0d821020fa241389cac3b3f6473eb5bdec18d03851ec5e90b623d512f436",
  "domain": "Computational Chemistry",
  "hardness_fn": {
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    "regime": "Well-posed forward; force field validity limits accuracy.",
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  "physics_fingerprint": {
    "L_DAG": 3.0,
    "carrier": "none",
    "difficulty_delta": 3,
    "domain": "Computational Chemistry",
    "integration_axis": "time",
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    "sensing_mechanism": "md_observable",
    "solution_space": "atomic_trajectory",
    "sub_domain": "Empirical force-field dynamics",
    "title": "Classical Molecular Dynamics"
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  "size_tiers": {
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    "center_spec": {
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      "forward_operator": "classical_md_forward",
      "input_format": "measurement_only",
      "omega": {
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        "ff": "AMBER"
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    "omega_bounds": {
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      "N_steps": [
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      "T_K": [
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      ],
      "dt_fs": [
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        10
      ],
      "ff": [
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        "CHARMM",
        "OPLS",
        "GROMOS",
        "ReaxFF"
      ]
    }
  },
  "staked_pwm": 0.0,
  "status": "testnet",
  "sub_domain": "Empirical force-field dynamics",
  "title": "Classical Molecular Dynamics"
}

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