molecular-dynamics

name	molecular-dynamics
description	Concept skill for Molecular Dynamics (MD) simulation. Describes MD ensembles, key parameters, and which tool skills to invoke for MD runs. Use this to understand MD concepts before selecting a specific simulation tool.
metadata	{"dependent_skills":["ase","mattersim"],"tags":["MD","molecular-dynamics","NVT","NPT","simulation","exploration"]}

Molecular Dynamics (MD) Simulation

Molecular Dynamics simulates the time evolution of a system of atoms by numerically integrating Newton's equations of motion under a given interatomic potential (force field). In the MLFF/PFD context, MD is primarily used for configuration space exploration — generating diverse, physically relevant structures for labeling and training.

Ensembles

Ensemble	Fixed Variables	Use Case
NVT	N, V, T	Fixed-volume exploration; most common for PFD
NPT	N, P, T	Variable-cell exploration; use when volume relaxation matters
NVE	N, V, E	Microcanonical; rarely used for exploration

Key Parameters

Parameter	Default (PFD)	Description
Temperature	300 K	Higher T increases structural diversity
Timestep	2 fs	Standard for most solids and liquids
Total steps	500 (≈1 ps)	Minimum for initial exploration
Save interval	50 steps	Frames saved for entropy-based curation
Pressure	0 GPa	NPT only

When to Use MD in a Workflow

• PFD fine-tuning / distillation: Step 2 — run MD with the current MLFF to generate candidate structures.
• Materials validation: Run short MD to check structural stability at target temperature.
• Property sampling: Generate an ensemble of configurations for property averaging.

Available Tool Skills

Skill	Best For
ase	MD with a trained DeePMD potential via ASE
mattersim	MD with the pre-trained MatterSim universal potential

Load the appropriate tool skill for step-by-step instructions (e.g., load_skill("ase")).