Related Experiment Video
Updated: Jun 27, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit
H Lee Woodcock1, Wenjun Zheng, An Ghysels
1Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. hlwood@nih.gov
Abstract:
A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the "tip effect" in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method.
More Related Videos
11:03An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
Published on: December 4, 2017
09:43Interfacial Molecular-level Structures of Polymers and Biomacromolecules Revealed via Sum Frequency Generation Vibrational Spectroscopy
Published on: August 13, 2019
Related Concept Videos
IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration
According to Hooke's law, the vibrational frequency is directly proportional to the...
IR Spectroscopy: Molecular Vibration Overview
Stretching vibrations are vibrational motions that occur along the bond line, changing the bond length or distance between two bonded atoms. They are further distinguished as symmetric or asymmetric. In symmetric stretching, the...
IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations
Problem Solving: Energy in Simple Harmonic Motion
Consider the spring in a shock absorber of a car. The spring attached to the wheel executes simple harmonic motion while the car is moving on a bumpy road. The force on the...
Energy in Simple Harmonic Motion
¹H NMR: Interpreting Distorted and Overlapping Signals
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...