Forblaze MD Sandbox Documentation

1. Overview

Forblaze MD Sandbox is a simulation sandbox that performs real-time molecular dynamics (MD) calculations directly in your browser, allowing for instant visualization and manipulation of the system.

2. Key Features

• Real-time Calculation: Continuous MD execution within the browser.
• Interactive Manipulation: Directly grab and move atoms with your mouse.
• Environmental Control: Adjust temperature, pressure, and time steps in real-time.
• Presets: Instantly build representative models such as Argon, Water, and Sodium Chloride.

3. Technical Specifications

The computation and rendering engines are written in Rust and executed via WebAssembly (WASM) and WebGPU, achieving high performance near that of native applications.

4. Notes on Approximations

To maintain real-time performance while ensuring practical accuracy, the following algorithms and approximations are employed:

Electrostatic Interactions (Real-space Approximation)

To minimize computational overhead, we use the Damped Shifted Force (DSF) method. It approximates interactions in real space using a screened potential and a cutoff.

Ensemble Control (Weak Coupling Method)

Temperature and pressure control (thermostat and barostat) are implemented using the Berendsen method (weak coupling method).

Intramolecular Potentials and Constraints

Bonds and angles are described using simple Harmonic potentials. Rigid constraints (such as SHAKE) are not applied.