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Last updated: 2024/01/01
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Installation

Installation on Linux

Difficulty: ★☆☆☆☆
Installing SPONGE and its companion software (Xponge and VMD) on Linux

Installation on Windows

Difficulty: ★☆☆☆☆
Installing SPONGE and its companion software (Xponge and VMD) on Windows

Modeling

Modeling the 4B1Y System

Difficulty: ★★★☆☆
Modeling the 4B1Y protein system, including ATP, the LAB ligand, and Mg ions, with Xponge

Modeling Polyethylene Glycol

Difficulty: ★★★☆☆
Modeling polymer materials with Xponge, using polyethylene glycol in the GAFF force field as an example

Basics

Folding of Alanine Dodecapeptide

Difficulty: ★★☆☆☆
Simulating alanine dodecapeptide folding in implicit solvent through Xponge modeling -> SPONGE simulation -> VMD visualization

Simulation of Sodium Chloride Crystals under High Pressure

Difficulty: ★★☆☆☆
Simulating sodium chloride crystals at 40 GPa through Xponge modeling -> SPONGE simulation -> VMD visualization

Enhanced Sampling of the Hydrogen Peroxide Dihedral Angle

Difficulty: ★★★☆☆
Using umbrella sampling, metadynamics, and SITS to perform enhanced sampling of the hydrogen peroxide dihedral angle