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

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

981
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...
981
Equilibrium Conditions for a Particle01:23

Equilibrium Conditions for a Particle

2.4K
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...
2.4K
Atomic Nuclei: Types of Nuclear Relaxation01:28

Atomic Nuclei: Types of Nuclear Relaxation

1.1K
Nuclear relaxation restores the equilibrium population imbalance and can occur via spin–lattice or spin–spin mechanisms, which are first-order exponential decay processes.
In spin–lattice or longitudinal relaxation, the excited spins exchange energy with the surrounding lattice as they return to the lower energy level. Among several mechanisms that contribute to spin–lattice relaxation, magnetic dipolar interactions are significant. Here, the excited nucleus transfers...
1.1K
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

1.2K
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
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...
1.2K
Molecular Orbital Theory II03:51

Molecular Orbital Theory II

21.5K
Molecular Orbital Energy Diagrams
21.5K
IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration01:16

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

3.2K
A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
According to Hooke's law, the vibrational frequency is directly proportional to...
3.2K

You might also read

Related Articles

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

Sort by
Same author

Subjective cognition trajectories, Alzheimer biomarkers, and incident mild cognitive impairment.

The journal of prevention of Alzheimer's disease·2026
Same author

Evaluation of fully automated ApoE4 proteotyping for <i>APOE</i> ε4 genotype estimation in the FINDERI cohort.

Alzheimer's & dementia (Amsterdam, Netherlands)·2026
Same author

Data Management and Analysis of Metal-Organic Framework Synthesis Using Data Models.

Journal of chemical information and modeling·2026
Same author

Intrathecal Kappa Free Light Chains in Relation to IgM Synthesis and MRZH Reaction in a Mixed Neurological Cohort.

Journal of neurochemistry·2026
Same author

Subjective cognition trajectories, Alzheimer biomarkers, and incident mild cognitive impairment.

medRxiv : the preprint server for health sciences·2026
Same author

Efficient Prediction of Multicomponent Adsorption Isotherms and Enthalpies of Adsorption in MOFs Using Classical Density Functional Theory.

The journal of physical chemistry. B·2026

Related Experiment Video

Updated: Apr 22, 2026

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the &#181;s-ms Timescale
08:09

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

4.8K

Time-averaged order parameter restraints in molecular dynamics simulations.

Niels Hansen1, Fabian Heller, Nathan Schmid

  • 1Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland, hansen@itt.uni-stuttgart.de.

Journal of Biomolecular NMR
|October 15, 2014
PubMed
Summary
This summary is machine-generated.

This study introduces a new molecular dynamics method to accurately simulate experimental order parameters. The technique effectively enforces order parameters without significantly altering atomic coordinate fluctuations in complex protein systems.

More Related Videos

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.5K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

1.0K

Related Experiment Videos

Last Updated: Apr 22, 2026

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the &#181;s-ms Timescale
08:09

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

4.8K
Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.5K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

1.0K

Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Modeling

Background:

  • Experimental order parameters (S(2)) provide crucial information on molecular dynamics.
  • Accurately incorporating these experimental values into molecular dynamics (MD) simulations remains a challenge.

Purpose of the Study:

  • To develop and validate a novel method for enforcing experimental S(2) order parameters as time-averaged quantities in MD simulations.
  • To investigate the key parameters controlling time-averaged restraints.

Main Methods:

  • A new restraining method was developed to enforce time-averaged S(2) order parameters.
  • The method's parameters (memory relaxation time and restraining potential weight) were systematically investigated.
  • Model systems (restrained vector, pentapeptide) and a realistic protein system (B3 domain of protein G) were used for validation.

Main Results:

  • The method successfully enforced backbone N-H order parameters for individual residues in a pentapeptide.
  • Spatial fluctuations of atomic coordinates were not significantly perturbed by the applied restraints.
  • The method's applicability was demonstrated on the B3 domain of protein G in aqueous solution.

Conclusions:

  • The developed method provides a robust way to integrate experimental S(2) order parameters into MD simulations.
  • This approach allows for more accurate modeling of molecular dynamics, particularly for systems like protein G.
  • The findings facilitate enhanced accuracy in computational biophysics and molecular modeling studies.