# Md

> Prepare SIESTA 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.

- Skill: `jinzhezenggroup/md-3` (Agent Skill)
- Install (CLI): `npx skillmds@latest add jinzhezenggroup/md-3`
- Raw SKILL.md: https://api.skillmd.com/api/skills/jinzhezenggroup/md-3/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Productivity
- License: MIT
- Author: jinzhezenggroup (https://skillmd.com/u/jinzhezenggroup)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/jinzhezenggroup/md-3

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# SIESTA MD (Subskill)

## Scope

This skill prepares MD tasks only.

It should generate:

- MD-capable SIESTA input
- ensemble/integrator/thermostat controls
- trajectory/output policy

It should not submit or execute jobs.

## Must provide

- structure input
- basis/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

1. MD-task input layout
1. MD control summary and assumptions
1. unresolved choices for confirmation
1. handoff note to `dpdisp-submit` if execution is requested