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Updated: May 7, 2026

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NAMDでガウス加速分子力学シミュレーションを実行する [Article v1.0]

Haley M Michel1, Marcelo D Polêto1, Justin A Lemkul1,2

  • 1Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, 24061, United States.

Living journal of computational molecular science
|August 22, 2025
PubMed
まとめ

ガウス加速分子ダイナミクス (GaMD) は,より迅速な自由エネルギー景観探索のためのエネルギー障壁を減らすことで分子シミュレーションを強化します. このチュートリアルでは,生物分子システムの GaMD シミュレーションと分析に関する実用的なガイドを提供します.

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Angular Momentum: Single Particle

Angular momentum is directed perpendicular to the plane of the rotation, and its magnitude depends on the choice of the origin. The perpendicular vector joining the linear momentum vector of an object to the origin is called the “lever arm.” If the lever arm and linear momentum are collinear, then the magnitude of the angular momentum is zero. Therefore, in this case, the object rotates about the origin such that it lies on the rim of the circumference defined by the lever arm magnitude.
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Van der Waals Equation

The ideal gas law is an approximation that works well at high temperatures and low pressures. The van der Waals equation of state (named after the Dutch physicist Johannes van der Waals, 1837−1923) improves it by considering two factors.
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Distribution of Molecular Speeds

The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...
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Maxwell-Boltzmann Distribution: Problem Solving

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Equilibrium Conditions for a Particle

When an object is in equilibrium, it is either at rest or moving with a constant velocity. There are two types of equilibrium: static and dynamic. Static equilibrium occurs when an object is at rest, while dynamic equilibrium occurs when an object is moving with a constant velocity. In both cases, there must be a balance of forces acting on the object.
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