Computational-chemistry-agent-skills 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.

install

source · Clone the upstream repo

git clone https://github.com/jinzhezenggroup/computational-chemistry-agent-skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/quantum-chemistry/dft-siesta/md" ~/.claude/skills/jinzhezenggroup-computational-chemistry-agent-skills-md-617de1 && rm -rf "$T"

manifest: quantum-chemistry/dft-siesta/md/SKILL.md

source content

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

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