Astropy
zLanqing/codex-claude-academic-skills
Comprehensive Python library for astronomy and astrophysics.
Prepare ABINIT molecular-dynamics task inputs from a user-provided structure and MD controls.
Install Md
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill md -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills md --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/quantum-chemistry/dft-abinit/md .claude/skills/md && rm -rf skills-srcUse ~/.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/
Install the "md" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/quantum-chemistry/dft-abinit/md into .claude/skills/md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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 install https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/quantum-chemistry/dft-abinit/mdType 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.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill md -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills md --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/quantum-chemistry/dft-abinit/md .agents/skills/md && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "md" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/quantum-chemistry/dft-abinit/md into .agents/skills/md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill md -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills md --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/quantum-chemistry/dft-abinit/md .cursor/skills/md && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "md" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/quantum-chemistry/dft-abinit/md into .cursor/skills/md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git --path quantum-chemistry/dft-abinit/md--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill md -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills md --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/quantum-chemistry/dft-abinit/md .gemini/skills/md && rm -rf skills-srcUse ~/.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/
Install the "md" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/quantum-chemistry/dft-abinit/md into .gemini/skills/md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills mdInstalls 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).
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill md -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/quantum-chemistry/dft-abinit/md .github/skills/md && rm -rf skills-srcUse ~/.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/
Install the "md" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/quantum-chemistry/dft-abinit/md into .github/skills/md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill md -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills md --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/quantum-chemistry/dft-abinit/md .opencode/skills/md && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "md" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/quantum-chemistry/dft-abinit/md into .opencode/skills/md/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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
md- GitHub stars
- 148
- Token cost
- ~296 tokens
- SKILL.md length
- 86 words
- Files
- 1
- Skills in repo
- 62
- Repo updated
- First seen
- Licence
- MIT
At a glance
Prepare ABINIT molecular-dynamics task inputs from a user-provided structure and MD controls.
- Works in 4 steps: MD-task input layout → MD control summary and assumptions → unresolved choices for confirmation → …
- The user needs finite-temperature trajectories with explicit ensemble
- SKILL.md covers Scope, Must provide, Usually should be explicit and Expected output
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Md is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. Prepare ABINIT molecular-dynamics task inputs from a user-provided structure and MD controls. Use when the user needs finite-temperature trajectories with explicit ensemble, timestep, and thermostat controls.
Its SKILL.md is about 300 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts. Compatibility notes: Requires a user-provided structure, suitable pseudopotentials, and runnable ABINIT environment.
It sits in Research & Science, covering Physical and earth sciences. The repository describes itself as: Agent skills to run computational-chemistry tasks, used in OpenClaw. The licence is MIT.
When your agent uses it
- The user needs finite-temperature trajectories with explicit ensemble
- Thermostat controls
Example prompts
- “/md”
Requirements
- Compatibility (from SKILL.md): Requires a user-provided structure, suitable pseudopotentials, and runnable ABINIT environment.
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- MD-task input layout
- MD control summary and assumptions
- unresolved choices for confirmation
- handoff note to dpdisp-submit if execution is requested
What it can do on your machine
Read from SKILL.md and the folder at commit 5c19e75. 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
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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.
Compatibility
Requires a user-provided structure, suitable pseudopotentials, and runnable ABINIT environment.
From compatibility in the SKILL.md frontmatter.
Context cost
Md loads about 296 tokens when it runs. Until then it costs about 53 tokens; SKILL.md has 86 words of instructions outside code blocks.
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); files beside SKILL.md are not scanned.
SKILL.md
The full file from jinzhezenggroup/computational-chemistry-agent-skills at commit 5c19e75, republished under its MIT licence (© jinzhezenggroup). 86 words, ~296 tokens.
Download SKILL.mdSave it as
.claude/skills/md/SKILL.md (or your agent's skills folder).- name
- md
- description
- Prepare ABINIT molecular-dynamics task inputs from a user-provided structure and MD controls. Use when the user needs finite-temperature trajectories with explicit ensemble, timestep, and thermostat controls.
- compatibility
- Requires a user-provided structure, suitable pseudopotentials, and runnable ABINIT environment.
- license
- MIT
- catalog-hidden
- true
- metadata.author
- qqgu
- metadata.version
- 0.1.0
- metadata.repository
- https://github.com/abinit/abinit
ABINIT MD (Subskill)
Scope
This skill prepares MD tasks only.
It should generate:
- MD-capable ABINIT input
- ensemble/integrator/thermostat controls
- trajectory/output policy
It should not submit or execute jobs.
Must provide
- structure input
- pseudopotential set choice
- timestep and number of steps
- ensemble intent (
NVE/NVT/NPT) - temperature/pressure control policy
Usually should be explicit
- initial velocity policy
- output stride for energies/trajectory
- charge/spin and SCF policy
Expected output
- MD-task input layout
- MD control summary and assumptions
- unresolved choices for confirmation
- handoff note to
dpdisp-submitif execution is requested
© jinzhezenggroup, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in quantum-chemistry/dft-abinit/md of jinzhezenggroup/computational-chemistry-agent-skills.
Open the folder on GitHubat commit 5c19e75
Compare with similar skills
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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Md this skilljinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~296 | Automated safety check: Pass | MIT | |
| AstropyzLanqing/codex-claude-academic-skills | 4.7k | 13 repos | ~2.9k | Automated safety check: Pass | BSD-3-Clause | |
| PymatgenzLanqing/codex-claude-academic-skills | 4.7k | 11 repos | ~5k | Automated safety check: Pass | MIT | |
| Cantera Ignition DelayK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.2k | Automated safety check: Pass | MIT | |
| Weathertrpc-group/trpc-agent-go | 1.9k | 8 repos | ~591 | Automated safety check: Pass | Apache-2.0 | |
| Pymol VisualizationChatMol/ChatMol | 373 | — | ~1.2k | Automated safety check: Pass | MIT |
Similar skills
Pymatgen
zLanqing/codex-claude-academic-skills
Materials science toolkit. An agent skill from zLanqing/codex-claude-academic-skills.
Cantera Ignition Delay
K-Dense-AI/scientific-agent-skills
Runs Cantera constant-volume or constant-pressure ignition simulations and reports temperature-based ignition delay with mechanism provenance and checks.
Weather
trpc-group/trpc-agent-go
Get current weather and forecasts via wttr.in or Open-Meteo.
Pymol Visualization
ChatMol/ChatMol
Generate publication-quality molecular visualization images using PyMOL.
Review
Muuuun/luxas
Write domain-authentic review articles that synthesize rather than stack.
More from jinzhezenggroup/computational-chemistry-agent-skills
All 62 skills in this repoQuantum ESPRESSO DFT Task Builder
jinzhezenggroup/computational-chemistry-agent-skills
Turns a user-supplied atomic structure and DFT settings into a runnable Quantum ESPRESSO input file, stopping short of submitting the job.
DP-GEN Simplify Workflow
jinzhezenggroup/computational-chemistry-agent-skills
Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs.
LAMMPS with DeePMD-kit
jinzhezenggroup/computational-chemistry-agent-skills
Prepares and runs molecular dynamics simulations in LAMMPS with a DeePMD machine-learning potential, writing the input script and choosing NVE, NVT or NPT.
LAMMPS ReaxFF Setup
jinzhezenggroup/computational-chemistry-agent-skills
Prepares and explains LAMMPS input scripts for reactive molecular dynamics with the ReaxFF potential, including charge equilibration and ensemble choice.
RDKit Conformer Generator
jinzhezenggroup/computational-chemistry-agent-skills
Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails.
RDKit Descriptors and Fingerprints
jinzhezenggroup/computational-chemistry-agent-skills
Computes RDKit physicochemical descriptors and molecular fingerprints from SMILES through a uv-run CLI script that skips and logs invalid molecules.
Related
Categories
Questions about Md
What does Md do?
Prepare ABINIT molecular-dynamics task inputs from a user-provided structure and MD controls. Md is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. Prepare ABINIT molecular-dynamics task inputs from a user-provided structure and MD controls.
When should I use Md?
Md fits situations like: the user needs finite-temperature trajectories with explicit ensemble; thermostat controls.
How do I install Md in Claude Code?
Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill md -a claude-code`. Or copy the skill folder (quantum-chemistry/dft-abinit/md in jinzhezenggroup/computational-chemistry-agent-skills) into .claude/skills/md in your project. Claude Code loads it when a task matches its description.
How do I install Md in Codex?
Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill md -a codex`. Or copy the skill folder (quantum-chemistry/dft-abinit/md in jinzhezenggroup/computational-chemistry-agent-skills) into .agents/skills/md in your project. Codex loads it when a task matches its description.
Can I use 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 jinzhezenggroup/computational-chemistry-agent-skills --skill 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/md, .gemini/skills/md, .github/skills/md and .opencode/skills/md in your project.
What does Md need to run?
SKILL.md names no scripts, command-line tools or credentials: Md is instructions for the agent only. Compatibility (from SKILL.md): Requires a user-provided structure, suitable pseudopotentials, and runnable ABINIT environment..
Does Md access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is 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. Review the folder before installing.
What licence does Md use?
Md is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Md use?
About 296 tokens (SKILL.md is roughly 1.2k 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 Md?
Skills that share tags, products or a category with Md: Astropy (zLanqing/codex-claude-academic-skills, 4.7k stars), Pymatgen (zLanqing/codex-claude-academic-skills, 4.7k stars), Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars) and Weather (trpc-group/trpc-agent-go, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Md?
jinzhezenggroup (a GitHub organization) maintains it in jinzhezenggroup/computational-chemistry-agent-skills, which has 148 GitHub stars. The repository holds 62 skills in this directory. The repository was last updated on October 9, 2026.
Source: jinzhezenggroup/computational-chemistry-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.