What is chem-solution-md?

A workflow for simulating molecules moving through liquid solvent. It builds solvent boxes, runs molecular dynamics—the computer simulation of particle movement—and measures properties such as structure, density, and diffusion.

Use it to prepare solvent boxes, run simulations at fixed pressure or volume, and analyse radial distributions, coordination, density convergence, and mean-square displacement.

It provides a repeatable process for studying molecules in solution instead of only in empty space or as static structures.

chem-solution-md — Skill by learningmatter-mit

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods

npx agentmods add skills/learningmatter-mit/atomisticskills/chem-solution-md

Any agent

npx skills add learningmatter-mit/AtomisticSkills --skill chem-solution-md

Clone the repo

git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills

Made for: Claude Code, Codex.

Per session 30 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,947 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. Scan, not verified.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5	$0.00030	$0.01947
Opus 5	$0.00015	$0.00974
Sonnet 5	$0.00006	$0.00389
Haiku 4.5	$0.00003	$0.00195

Measured 2d ago against content hash bfd49daed408, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

chem-solution-md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (scripts/analyze_solution_md.py, scripts/build_solvation_box.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.agents/skills/chem-solution-md/SKILL.md · 190 lines

How it starts

The opening of the file, as written. The whole thing — 190 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Solution-Phase Molecular Dynamics

Goal

Set up and run molecular dynamics (MD) simulations of molecules in explicit solvent. This skill covers three stages: (1) building a solvation box with Packmol, (2) running NPT/NVT MD using MLIPs, and (3) analyzing the trajectory for radial distribution functions (RDFs), coordination numbers, density convergence, and mean-square displacement (MSD).

[!IMPORTANT] This skill bridges gas-phase chem-* skills and condensed-phase mat-* skills by providing workflows for solvation dynamics, liquid structure characterization, and dissolution studies.

1. Prerequisites

Packmol binary must be installed and on PATH in the base-agent environment.
RDKit must be available in the base-agent environment (for SMILES → 3D geometry).
An MLIP backend must be available via MCP tools (MACE, MatGL, or FairChem).

2. MLIP Selection

Refer to the foundation-potentials skill for model selection.

[!NOTE]

Organic solvents: Use MACE-MH-1 with omol head, or UMA with omol task.

Aqueous inorganic systems: Use MACE-MH-1 with omat_pbe head, or MatGL/CHGNet.

Mixed organic-inorganic: Use UMA which handles both.

3. Workflow

Step 1: Build Solvation Box

Use the box-building script to create a solvated system with Packmol:

# Env: base-agent
# Pure solvent box (64 water molecules)
python .agents/skills/chem-solution-md/scripts/build_solvation_box.py \
    --solvent water \
    --num_solvent 64 \
    --output_dir research/my_folder/solvation_box

# Solute in solvent (NaCl in 64 water molecules)
python .agents/skills/chem-solution-md/scripts/build_solvation_box.py \
    --solute_smiles "[Na+].[Cl-]" \
    --solvent water \
    --num_solvent 64 \
    --output_dir research/my_folder/solvation_box

Key Parameters:

Argument	Description
`--solvent`	Pre-defined solvent name (see available solvents below)
`--solvent_smiles`	SMILES string for custom solvent
`--solvent_file`	Path to solvent structure file
`--solute_smiles`	SMILES string for solute (optional)
`--solute_file`	Path to solute structure file (optional)
`--num_solvent`	Number of solvent molecules (default: 64)
`--box_size`	Cubic box side in Å (auto-calculated from density if omitted)
`--tolerance`	Minimum inter-molecular distance in Å (default: 2.0)
`--output_dir`	Output directory

Read the full file on GitHub · 190 lines

Files

What ships with it

13 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2d ago First seen · 190 lines · 30 tokens per session scan A bfd49daed408

Subscribe to this mod's changes

chem-solution-md is a skill published in the GitHub repository learningmatter-mit/AtomisticSkills (154 stars, last pushed 7d ago), licensed MIT. It adds 30 tokens to every session and 1,947 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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chem-solution-md