Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Molecular Weight of Step-Growth Polymers01:08

Molecular Weight of Step-Growth Polymers

2.2K
Step growth polymerization involves bi or multifunctional monomers. Bifunctional monomers react to form linear step growth polymers, whereas multifunctional monomers react to form non-linear or branched polymers.
As the step-growth polymerization involves step-wise condensation of monomers, the molecular weight also builds up eventually. Consequently, high molecular weight polymers are obtained at the late stages of the polymerization, where 99% of monomers have been consumed.
The extent of the...
2.2K
Mean free path and Mean free time01:22

Mean free path and Mean free time

3.6K
Consider the gas molecules in a cylinder. They move in a random motion as they collide with each other and change speed and direction. The average of all the path lengths between collisions is known as the "mean free path."
3.6K
Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

4.0K
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...
4.0K
Typical Model Studies01:30

Typical Model Studies

359
Fluid mechanics model studies often utilize scaled-down systems to predict fluid behavior in full-scale environments, such as river flows, dam spillways, and structures interacting with open surfaces. Maintaining Froude number similarity in river models is crucial, as it replicates surface flow features like wave patterns and velocities.
359
Maxwell-Boltzmann Distribution: Problem Solving01:20

Maxwell-Boltzmann Distribution: Problem Solving

1.5K
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
1.5K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

847
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
847

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Rotational memory function of SPC/E water.

The Journal of chemical physics·2026
Same author

Harnessing Quantum Computing for Energy Materials: Opportunities and Challenges.

ACS energy letters·2026
Same author

Equipartition and the Temperature of Maximum Density of TIP4P/2005 Water.

The journal of physical chemistry. B·2026
Same author

Extended molecular eigenmodes treatment of dipole-dipole NMR relaxation in real fluids.

The Journal of chemical physics·2025
Same author

Molecular-Level Insights into the NMR Relaxivity of Gadobutrol Using Quantum and Classical Molecular Simulations.

Chemical & biomedical imaging·2025
Same author

Consequences of the failure of equipartition for the <i>p</i>-<i>V</i> behavior of liquid water and the hydration free energy components of a small protein.

Chemical science·2025

Related Experiment Video

Updated: Jul 6, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.8K

MD Simulation of Water Using a Rigid Body Description Requires a Small Time Step to Ensure Equipartition.

Dilipkumar N Asthagiri1, Thomas L Beck1

  • 1Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, Tennessee 37830-6012, United States.

Journal of Chemical Theory and Computation
|December 29, 2023
PubMed
Summary
This summary is machine-generated.

Using longer time steps in water simulations disrupts energy balance between molecular motion types. Shorter time steps are crucial for accurately capturing rotational dynamics and thermodynamic properties in aqueous systems.

More Related Videos

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.3K
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

4.5K

Related Experiment Videos

Last Updated: Jul 6, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.8K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.3K
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

4.5K

Area of Science:

  • Computational chemistry and physics
  • Molecular dynamics simulations
  • Aqueous systems

Background:

  • Simulations of aqueous systems often freeze bond vibrations and angle bending in water.
  • This allows for longer integration time steps (δt), commonly using δt = 2 fs for rigid water models.
  • The assumption is that freezing vibrations simplifies calculations without significant physical impact.

Purpose of the Study:

  • To investigate the impact of varying time steps (δt) on the equipartition of energy in molecular dynamics simulations of water.
  • To understand the reasons for the lack of equipartition between translational and rotational modes.
  • To assess the influence of time step on rotational relaxation dynamics and thermodynamic properties.

Main Methods:

  • Simulated the SPC/E model of water using a range of time steps from 0.5 fs to 3.0 fs, and up to 4 fs with hydrogen mass repartitioning.
  • Analyzed the autocorrelation of translational center-of-mass velocity and angular velocity.
  • Examined the fluctuation-dissipation relation and its implications for energy equipartition and thermodynamic properties.

Main Results:

  • Equipartition between translational and rotational modes was not achieved for δt ≥ 0.5 fs, with rotational modes showing lower temperatures.
  • Rotational relaxation occurs on a timescale comparable to vibrational periods, challenging the rationale for freezing vibrations.
  • Time steps δt ≥ 1 fs inaccurately capture fast rotational relaxation, effectively slowing it down and impacting thermodynamic properties like potential energy and excess hydration entropy.

Conclusions:

  • The choice of time step significantly affects the accuracy of molecular dynamics simulations for water, particularly concerning rotational dynamics and energy equipartition.
  • Shorter time steps (e.g., 0.5 fs) are necessary to accurately capture fast rotational relaxation and ensure reliable thermodynamic property calculations.
  • The study highlights the importance of considering the temporal evolution of fluctuations and the limitations imposed by time step choices in equilibrium molecular dynamics.