# ⚛  L1 Principle — Coarse-Grained Molecular Dynamics (MARTINI, Dry-MARTINI)

**ID:** `L1-306` · **Status:** ⊙ Testnet (genesis catalog)

> **🌐 Domain:** Computational Chemistry — *Multi-atom grouping force fields*
> **🎯 Problem class:** nonlinear inverse · **🧮 Solution space:** coarse grained trajectory
> **📡 Carrier:** none · **🌫 Noise:** thermal langevin
> **⚖ Difficulty (δ):** 3 · **⛓ Block:** 41554115

---

## 🧠 1. Introduction

**Coarse-Grained Molecular Dynamics (MARTINI, Dry-MARTINI)** is a **nonlinear inverse problem** whose unknown lives in **coarse grained trajectory** space, within the **Multi-atom grouping force fields** sub-domain of **Computational Chemistry**.

Measurements consist of none via a **md observable** sensing mechanism.

The forward operator applies, in order: E · bead mapping operator; E · CG forcefield operator; D · time · symplectic operator; O · mesoscale observable operator.

Observations are corrupted by Langevin-type thermal fluctuations. Well-posed forward; transferability limited to similar chemistries.

## ⚙ 2. Forward Model

Physical chain: **x** → E · bead mapping → E · CG forcefield → D · time · symplectic → O · mesoscale observable → **y** (detector).

```
y = `O.mesoscale_observable` `D.time.symplectic` `E.CG_forcefield` `E.bead_mapping` x
```

**Measurement DAG:**

| Primitive | What it does |
|---|---|
| `E.bead_mapping` | E · bead mapping operator |
| `E.CG_forcefield` | E · cg forcefield operator |
| `D.time.symplectic` | D · time · symplectic operator |
| `O.mesoscale_observable` | O · mesoscale observable operator |

## 🔬 3. Physics Fingerprint

| Property | Value |
|---|---|
| Domain | Computational Chemistry |
| Sub domain | Multi-atom grouping force fields |
| Carrier | none |
| Problem class | nonlinear_inverse |
| Solution space | coarse_grained_trajectory |
| Noise model | thermal_langevin |
| Integration axis | time |
| Difficulty delta | 3 |
| L dag | 3.1 |

## 📡 4. Measurement Model

Well-posed forward; transferability limited to similar chemistries.

| Metric | Value |
|---|---|
| Metric | rdf_L2_CG |
| Secondary | membrane_thickness_error_nm |

## 📏 5. Operating Range (Ω)

**Center problem class:** `coarse_grained_md` · **Forward operator:** `cg_md_forward`

**Center point:**

| Parameter | Unit | Value |
|---|---|---|
| Ff | — | MARTINI_v3 |
| T k | — | 310 |
| Dt fs | — | 20 |
| N beads | — | 10000 |
| N steps | — | 1e+07 |

**Allowed bounds:**

| Parameter | Unit | Range |
|---|---|---|
| Ff | — | MARTINI_v2, MARTINI_v3, MSCG, PRIME20 |
| T k | — | 200 – 400 |
| Dt fs | — | 5 – 50 |
| N beads | — | 100 – 100000000.0 |
| N steps | — | 10000 – 10000000000.0 |

## 🎯 6. Tolerance (ε)

**Center tolerance:** g(r) L2 <= 0.03

| Metric | Range |
|---|---|
| Rdf l2 cg | 0.01 – 0.3 |

## ⚖ 7. Hardness Function

Hardness scales as **`epsilon_fn`** on **rdf_L2_CG**, with κ = `150` and δ = `3`.

## 💾 8. Reference Dataset

- **primary** · weight 1.0 · IPFS _(not pinned yet)_

## 9. On-chain Registration

- **Chain hash:** `0x2c7de354450547ba2ee4f3024bf4dfbea9b78b02af114ceccda8d2c41e97e88f`
- **Chain tx hash:** `0xa5bc62992a36e99f8831ac3e6343326edc7a72b100b9fcdbfc85e204d6d1358e`
- **Chain block:** `41554115`

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## File Mapping

This bundle consists of: `L1-306.md`, `L1-306.json`.

| File | Role | How to regenerate |
|------|------|-------------------|
| `L1-306.md` | Source of truth — edit this | Human or LLM |
| `L1-306.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 `L1-306`._
_Edit it, regenerate the JSON, and submit at [/submit](/submit) to claim the artifact._