Agent skill

Chem Solution Md

by learningmatter-mit in learningmatter-mit/AtomisticSkills

Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.

MITAuto-check passedResearch & Science

Install Chem Solution Md

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-solution-md -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills chem-solution-md --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chem-solution-md .claude/skills/chem-solution-md && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "chem-solution-md" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-solution-md into .claude/skills/chem-solution-md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-solution-md", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-solution-md

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

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

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills chem-solution-md --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/chem-solution-md .agents/skills/chem-solution-md && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "chem-solution-md" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-solution-md into .agents/skills/chem-solution-md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-solution-md", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

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

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills chem-solution-md --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/chem-solution-md .cursor/skills/chem-solution-md && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "chem-solution-md" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-solution-md into .cursor/skills/chem-solution-md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-solution-md", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/learningmatter-mit/AtomisticSkills.git --path skills/chem-solution-md

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-solution-md -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills chem-solution-md --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/chem-solution-md .gemini/skills/chem-solution-md && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "chem-solution-md" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-solution-md into .gemini/skills/chem-solution-md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-solution-md", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills chem-solution-md

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-solution-md -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/chem-solution-md .github/skills/chem-solution-md && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "chem-solution-md" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-solution-md into .github/skills/chem-solution-md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-solution-md", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

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

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills chem-solution-md --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/chem-solution-md .opencode/skills/chem-solution-md && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "chem-solution-md" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-solution-md into .opencode/skills/chem-solution-md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-solution-md", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: chem-solution-md
GitHub stars: 175
Token cost: ~1.9k tokens
SKILL.md length: 615 words
Files: 14 (incl. scripts)
Skills in repo: 129
Repo updated: Oct 6, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.

Works in 5 steps: Prerequisites → MLIP Selection → Workflow → …
Tasks that involve Physical and earth sciences
SKILL.md covers Goal, 1. Prerequisites, 2. MLIP Selection and 3. Workflow, plus 3 more sections
Runs Python scripts from its folder

What it does

Chem Solution Md is an agent skill from learningmatter-mit/AtomisticSkills. Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 18 other files, including scripts (for example `examples/Li_EC_MACE-MH-1/README.md`, `examples/Li_EC_MACE-MH-1/box_metadata.json` and `examples/Li_EC_MACE-MH-1/solution_analysis.json`).

It sits in Research & Science, covering Physical and earth sciences and Drug discovery and cheminformatics. It works with Model Context Protocol. The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.

When your agent uses it

Tasks that involve Physical and earth sciences
Tasks that involve Drug discovery and cheminformatics

Example prompts

“/chem-solution-md”

Requirements

Python 3

Workflow steps

5 steps, taken from the step headings in SKILL.md.

Prerequisites
MLIP Selection
Workflow
Examples
Constraints

What it can do on your machine

Read from SKILL.md and the folder at commit 7f2d86d. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 2 files in scripts/ (Python), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- doi.org
- pymatgen.org
- github.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Chem Solution Md loads about 1.9k tokens when it runs. Until then it costs about 40 tokens; SKILL.md has 615 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~40
When it runs · the whole SKILL.md, loaded when a task matches: ~1.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from learningmatter-mit/AtomisticSkills at commit 7f2d86d, republished under its MIT licence (© learningmatter-mit). 615 words, ~1,899 tokens.

Download SKILL.mdSave it as .claude/skills/chem-solution-md/SKILL.md (or your agent's skills folder). This skill also uses 13 other files; get the full folder from GitHub.

name: chem-solution-md
description: Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.
metadata.category: chemistry
metadata.venv: cpu, mlip

Solution-Phase Molecular Dynamics

<!-- mcp-tools-note -->

[!NOTE] Steps written server.tool are MCP tool calls: mace.load_model is the load_model tool of the mace server (mcp__mace__load_model, or mcp__plugin_atomistic-skills_mace__load_model when installed as a plugin). Without a connected server, run the same tools from the shell. Tools named in one command share a process, so a model loaded by load_model stays loaded:
bash
${CLAUDE_SKILL_DIR}/../../venv/run mlip python -m src.mcp_server.cli mace load_model key=value run_md key=value

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 for the cpu environment.
RDKit must be available in the cpu 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:

bash

# Pure solvent box (64 water molecules)
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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)
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/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

Available pre-defined solvents: water, methanol, ethanol, acetonitrile, dmso, dmf, thf, toluene, acetone, dichloromethane, chloroform, hexane

Output files:

solvated_box.cif — Periodic structure for MD
solvated_box.xyz — Non-periodic XYZ for visualization
box_metadata.json — Box size, atom counts, solute indices

Step 2: Run MD with MLIP

Use MCP run_md tools for NPT equilibration followed by NVT production.

NPT Equilibration (stabilize density):

bash

mace.load_model(
    model_name="MACE-MH-1",
    task_name="omol"
)
mace.run_md(
    structure_data="research/my_folder/solvation_box/solvated_box.cif",
    temperature=300,
    ensemble="npt",
    pressure=1.01325,        # 1 atm in bar
    steps=5000,              # 2.5 ps at 0.5 fs timestep
    timestep=0.5,            # 0.5 fs for systems with water (fast O-H vibrations)
    log_interval=10,
    monitor=True,
    monitor_type=["explosion", "volume"],
    output_dir="research/my_folder/npt_equilibration"
)

NVT Production (use the equilibrated structure):

bash

mace.run_md(
    structure_data="research/my_folder/npt_equilibration/final_structure.cif",
    temperature=300,
    ensemble="nvt",
    steps=20000,             # 10 ps at 0.5 fs timestep
    timestep=0.5,
    log_interval=10,
    monitor=True,
    monitor_type="explosion",
    output_dir="research/my_folder/nvt_production"
)

Show full SKILL.md (251 more words)Show less

Step 3: Analyze Trajectory

Run the analysis script on the production trajectory:

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/analyze_solution_md.py \
    --trajectory research/my_folder/nvt_production/trajectory.traj \
    --rdf_pairs "Na-O,Cl-O,O-O" \
    --msd_elements "Na,Cl" \
    --log_interval_fs 5.0 \
    --output_dir research/my_folder/analysis

Key Parameters:

Argument	Description
`--trajectory`	Path to ASE .traj trajectory file
`--rdf_pairs`	Comma-separated element pairs for RDF, e.g. `"Na-O,Cl-O"`
`--rmax`	Maximum RDF distance in Å (default: 8.0)
`--start_frame`	First frame to include in analysis (default: 0)
`--stride`	Frame stride (default: 1)
`--log_interval_fs`	Time between frames in fs (default: 10.0)
`--msd_elements`	Comma-separated elements for MSD (optional)

Output files:

solution_analysis.json — Full results (RDF data, coordination numbers, density, MSD)
rdf_plots.png — RDF plots for each element pair
density_convergence.png — Density vs. time
msd_plot.png — MSD for specified elements (if requested)

4. Examples

Pure Water Box

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/build_solvation_box.py \
    --solvent water --num_solvent 64 \
    --output_dir ${CLAUDE_SKILL_DIR}/examples/pure_water

Expected: 192 atoms (64 × 3), box ~12.4 Å

NaCl in Water

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/build_solvation_box.py \
    --solute_smiles "[Na+].[Cl-]" --solvent water --num_solvent 64 \
    --output_dir ${CLAUDE_SKILL_DIR}/examples/NaCl_in_water

After MD + analysis, expected RDF peak positions:

Na–O first peak: ~2.4 Å
Cl–O first peak: ~3.2 Å
Na coordination number: ~5–6

5. Constraints

Timestep: Use 0.5 fs for water and systems with O–H/N–H bonds (fast vibrations). Can use 1.0 fs for heavier solvents without H.
Equilibration: NPT equilibration is critical. Verify density stabilization before production run.
System size: A minimum of 64 solvent molecules is recommended for reliable RDFs. Larger boxes (128–256) reduce finite-size effects.
PBC interactions: Ensure the box is large enough that periodic images do not interact (box side > 2 × rmax for RDF).
Environments:
- cpu for box building and analysis scripts
- MCP tools for MD (any MLIP backend)

References

Martínez et al., "PACKMOL: A package for building initial configurations for molecular dynamics simulations", J. Comput. Chem., 2009. DOI
pymatgen PackmolBoxGen: pymatgen.io.packmol

Author: Bowen Deng Contact: GitHub @learningmatter-mit

Files

SKILL.md and 13 other files (scripts) in skills/chem-solution-md of learningmatter-mit/AtomisticSkills.

SKILL.md
examples/Li_EC_MACE-MH-1/README.md
examples/Li_EC_MACE-MH-1/box_metadata.json
examples/Li_EC_MACE-MH-1/density_convergence.png
examples/Li_EC_MACE-MH-1/rdf_plots.png
examples/Li_EC_MACE-MH-1/solution_analysis.json
examples/pure_water_MACE-MH-1/README.md
examples/pure_water_MACE-MH-1/box_metadata.json
examples/pure_water_MACE-MH-1/density_convergence.png
examples/pure_water_MACE-MH-1/rdf_plots.png
examples/pure_water_MACE-MH-1/solution_analysis.json
resources/common_solvents.yaml
scripts/analyze_solution_md.py
scripts/build_solvation_box.py

Open the folder on GitHubat commit 7f2d86d

Compare with similar skills

Chem Solution Md next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

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Questions about Chem Solution Md

What does Chem Solution Md do?

Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics. Chem Solution Md is an agent skill from learningmatter-mit/AtomisticSkills. Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.

When should I use Chem Solution Md?

Chem Solution Md fits situations like: tasks that involve Physical and earth sciences; tasks that involve Drug discovery and cheminformatics.

How do I install Chem Solution Md in Claude Code?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-solution-md -a claude-code`. Or copy the skill folder (skills/chem-solution-md in learningmatter-mit/AtomisticSkills) into .claude/skills/chem-solution-md in your project. Claude Code loads it when a task matches its description.

How do I install Chem Solution Md in Codex?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-solution-md -a codex`. Or copy the skill folder (skills/chem-solution-md in learningmatter-mit/AtomisticSkills) into .agents/skills/chem-solution-md in your project. Codex loads it when a task matches its description.

Can I use Chem Solution Md in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-solution-md -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chem-solution-md, .gemini/skills/chem-solution-md, .github/skills/chem-solution-md and .opencode/skills/chem-solution-md in your project.

What does Chem Solution Md need to run?

Going by SKILL.md and its folder, Chem Solution Md needs Python for the scripts in its folder. Our summary lists: Python 3.

Does Chem Solution Md access the network?

SKILL.md names 3 domains. As links in the text: doi.org, pymatgen.org and github.com. This is read from the text; nothing was executed.

Is Chem Solution Md safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Chem Solution Md use?

Chem Solution Md is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Chem Solution Md use?

About 1.9k tokens (SKILL.md is roughly 7.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Chem Solution Md?

Skills that share tags, products or a category with Chem Solution Md: Chemgraph (argonne-lcf/ChemGraph, 162 stars), Hcls Build Agent (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Tooluniverse (ynulihao/AgentSkillOS, 617 stars) and Chemgraph (argonne-lcf/ChemGraph, 162 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Chem Solution Md?

learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 175 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 6, 2026.

Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Chem Solution Md

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Solution-Phase Molecular Dynamics

Goal

1. Prerequisites

2. MLIP Selection

3. Workflow

Step 1: Build Solvation Box

Step 2: Run MD with MLIP

Step 3: Analyze Trajectory

4. Examples

Pure Water Box

NaCl in Water

5. Constraints

References

Files

Compare with similar skills

Similar skills

More from learningmatter-mit/AtomisticSkills

Related

Questions about Chem Solution Md