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Related Concept Videos

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.
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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 Particle01:23

Equilibrium Conditions for a Particle

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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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Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [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
Summary
This summary is machine-generated.

Gaussian-accelerated molecular dynamics (GaMD) enhances molecular simulations by reducing energy barriers for faster free energy landscape exploration. This tutorial provides a practical guide to GaMD simulations and analysis for biomolecular systems.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular dynamics

Background:

  • Enhanced sampling techniques are crucial for exploring complex biomolecular systems.
  • Gaussian-accelerated molecular dynamics (GaMD) offers a method to overcome energy barriers and accelerate conformational sampling.

Purpose of the Study:

  • To provide a comprehensive tutorial on applying GaMD simulations.
  • To guide users through the complete GaMD workflow, from setup to analysis.
  • To connect theoretical concepts of GaMD with practical implementation.

Main Methods:

  • Demonstration of GaMD on the alanine dipeptide model system.
  • Step-by-step instructions for conventional MD, GaMD equilibration, production, and reweighting.
  • Utilizing PyReweighting for free energy profile analysis.

Main Results:

  • Practical insights into input file preparation and GaMD convergence monitoring.
  • Successful application of GaMD to accelerate sampling of configurational space.
  • Generation of free energy profiles using reweighted data.

Conclusions:

  • GaMD is an effective technique for enhanced sampling in molecular dynamics.
  • This tutorial streamlines the GaMD workflow for researchers.
  • The methodology is applicable to a wide range of biomolecular systems.