MD Simulations · SMAD

MD Simulations

Initializing molecular dynamics engine…

⬡System Setup

Example system

Particles512

512

Box size (Å)40.0

40

📂

Drop structure file here
XYZ · PDB · POSCAR · LAMMPS · CIF

Or paste structure text

—

Supercell replication 1×1×1

× ×

No structure linked yet.

Supercell for linked structure

× ×

Initial temperature (K) ?Temperature used to assign Maxwell-Boltzmann velocity distribution at initialization.

300

Not initialized

⚛Force Field

Potential ?Lennard-Jones is standard for noble gases. Morse and Buckingham are common for ionic/covalent systems.

Cutoff (σ units) ?Interactions beyond this distance are truncated. Larger cutoffs improve accuracy but increase cost. 2.5σ is standard for LJ.

2.5

ReaxFF reactive force field is not active in the browser build. Use the LAMMPS export to run ReaxFF locally.

Machine-learning interatomic potentials (MACE, NequIP, CHGNet) — server-side integration planned.

◎Ensemble & Thermostat

Ensemble ?NVE: constant energy. NVT: constant temperature (thermostat). NPT: constant temperature + pressure (barostat).

Thermostat ?Langevin: stochastic friction + random force. Nosé-Hoover: extended system, better for sampling. Velocity rescale: simple but breaks microcanonical.

τ_T coupling time (ps)

↻Integration

Integrator

Timestep (fs) ?Typical: 1–2 fs for room-temperature simulations. Reduce for high-temperature or light atoms (H). Larger timestep = faster but may break energy conservation.

2.0

Total steps

Sample every

Boundary conditions ?Periodic in xyz: standard for bulk simulation. Open box: useful for clusters, surfaces, or visualization.

◈Visualization

Color by

Atom scale1.0

1.0

Show simulation box

Approximate bonds

Velocity vectors

Coordinate axes

◈On-the-fly Analysis

g(r) RDF MSD VACF Stress

RDF bins ?More bins = finer resolution g(r), but slower. 100-200 is typical.

r_max (Å)

● Idle

step 0 · 0.000 ps

Perspective

⬡

No system loaded

Choose a preset and click Initialize

Ortho · Top

Perspective

Top · Ortho

Front · Ortho

Right · Ortho

Perspective · Preview

T [K]

—

E_k/E_p/E_tot [eV]

—/—/—

P [bar]

—

ρ [g/cm³]

—

t [ps] · N

— · 0

📈

Energy vs time

Total, kinetic, and potential energy appear during simulation

🌡

Temperature vs time

Instantaneous T(t) and running average

⟂

Pressure vs time

Virial pressure from the stress tensor

〰️

Radial Distribution Function g(r)

Enable g(r) in Analysis panel — computed every sample step

⇥

Mean Squared Displacement

Enable MSD in Analysis panel to track diffusion coefficient D

〜

Velocity Autocorrelation

Enable VACF — Fourier transform gives phonon DOS

⊠

Stress tensor components

σ_xx, σ_yy, σ_zz, σ_xy, σ_xz, σ_yz

ID ↕	Type ↕	Position (x, y, z) Å	Von Mises Stress ↕	Vol. Strain ↕	CN ↕	Pot. E (eV) ↕	At. Vol. (Å³) ↕
Initialize a system to populate the particle table