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相关概念视频

Angular Momentum: Single Particle01:10

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.
The...
Van der Waals Equation01:10

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.
First, the attractive forces between molecules, which are stronger at higher densities and reduce the pressure, are considered by adding to the pressure a term equal to the square of the molar density multiplied by a positive coefficient a. Second, the volume...
Distribution of Molecular Speeds01:27

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...
Maxwell-Boltzmann Distribution: Problem Solving01:20

Maxwell-Boltzmann Distribution: Problem Solving

Individual molecules in a gas move in random directions, but a gas containing numerous molecules has a predictable distribution of molecular speeds, which is known as the Maxwell-Boltzmann distribution, f(v).
This distribution function f(v) is defined by saying that the expected number N (v1,v2) of particles with speeds between v1 and v2 is given by
Equilibrium Conditions for a Particle01:23

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.
To understand the concept of equilibrium, let us first consider the forces acting on an object. When different forces act on an object, they can...

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相关实验视频

Updated: May 7, 2026

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
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Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

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在NAMD中运行高斯加速分子动力学模拟 (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
概括

高斯加速分子动力学 (GaMD) 通过减少能量障碍来提高分子模拟的速度. 本教程为生物分子系统的GaMD模拟和分析提供了实用指南.

科学领域:

  • 计算化学
  • 生物物理
  • 分子动力学

背景情况:

  • 加强采样技术对于探索复杂的生物分子系统至关重要.
  • 高斯加速分子动力学 (GaMD) 提供了一种方法来克服能量障碍并加速构造性采样.

研究的目的:

  • 为应用GaMD模拟提供全面的教程.
  • 引导用户完成GaMD工作流程,从设置到分析.
  • 将GaMD的理论概念与实际实施联系起来.

主要方法:

  • 在二模型系统上演示GaMD.
  • 常规MD,GaMD平衡,生产和重量化的逐步说明
  • 使用PyReweighting进行自由能量分析.

主要成果:

  • 对输入文件准备和GaMD融合监测的实用见解.
  • 成功应用GaMD来加快配置空间的采样.
  • 使用重量化数据生成免费能源配置文件.

结论:

  • GaMD是一种有效的分子动力学增强采样技术.

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  • 这个教程简化了研究人员的GaMD工作流程.
  • 该方法适用于广泛的生物分子系统.