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

Conformity01:20

Conformity

48.2K
Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.
48.2K
Molecular Models02:00

Molecular Models

43.9K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
43.9K
Virtual Work01:20

Virtual Work

1.4K
The principle of virtual work states that if a body is in static and dynamic equilibrium, then the sum of all the virtual work done by all external forces and couple moments for any given virtual displacement must be zero.
In static equilibrium, a body can experience an imaginary or virtual movement, such as displacement or rotation. The virtual work done by a force is equal to the dot product of force and virtual displacement in the direction of the force. When it comes to virtually rotating a...
1.4K
Conformations of Butane02:20

Conformations of Butane

18.4K
Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
18.4K
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

19.9K
The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
19.9K
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

14.8K
Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
14.8K

You might also read

Related Articles

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

Sort by
Same author

Towards the International Conference on Biophysics and Biomedical Sciences: ICBBS 2026.

Biophysics and physicobiology·2026
Same author

Announcement of BPPB paper awards 2025.

Biophysics and physicobiology·2026
Same author

Affinity of drug candidates binding to SARS-CoV-2 PLpro assessed using a generalized-ensemble method.

Scientific reports·2026
Same author

Correction: Phenology analysis for trait prediction using UAVs in a MAGIC rice population with different transplanting protocols.

Frontiers in artificial intelligence·2025
Same author

Softness- and Pressure-Perceptive Electronic Skin with Reservoir-Computed Central Nervous System.

Small methods·2025
Same author

A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.

Biophysics and physicobiology·2025
Same journal

How Do DICER1 Syndrome Mutations Disrupt Catalysis? Unveiling Dicer Metal Binding Architecture and Mechanism of Action Using MD Simulations and QM/MM Calculations.

Journal of computational chemistry·2026
Same journal

Quadruple Bonding of Alkaline Earth Atoms in AeCLi<sub>4</sub> (Ae = Be - Ba) Complexes.

Journal of computational chemistry·2026
Same journal

From SMILES Codes for Reactants and Products to Transition States With VeloxChem.

Journal of computational chemistry·2026
Same journal

Electric-Field Effects on Structure and Conductance in a Cytochrome b<sub>562</sub> Junction.

Journal of computational chemistry·2026
Same journal

Quantum Chemistry Study of Luminescence Quenching in the Eu<sup>3+</sup>@UiO-67 Sensor Induced by Ag<sup>+</sup> Ions.

Journal of computational chemistry·2026
Same journal

Projection-Modified Direct Inversion in the Iterative Subspace: A Memory-Efficient Convergence Method for the Extended Molecular Ornstein-Zernike Theory.

Journal of computational chemistry·2026
See all related articles

Related Experiment Video

Updated: Feb 14, 2026

Spatial Separation of Molecular Conformers and Clusters
10:37

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

11.8K

Molecular dynamics coupled with a virtual system for effective conformational sampling.

Tomonori Hayami1, Kota Kasahara2, Haruki Nakamura1

  • 1Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

Journal of Computational Chemistry
|February 22, 2018
PubMed
Summary
This summary is machine-generated.

Virtual-system coupled canonical molecular dynamics (VcMD) enhances conformational sampling without estimating canonical distribution functions. This novel method accelerates molecular dynamics simulations for complex systems like peptide interactions.

Keywords:
all-atom modelcanonical samplingenhanced samplingfree-energy landscapereaction coordinate

More Related Videos

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

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

Published on: May 20, 2020

9.3K
Visualizing the Conformational Dynamics of Membrane Receptors Using Single-Molecule FRET
10:59

Visualizing the Conformational Dynamics of Membrane Receptors Using Single-Molecule FRET

Published on: August 17, 2022

3.8K

Related Experiment Videos

Last Updated: Feb 14, 2026

Spatial Separation of Molecular Conformers and Clusters
10:37

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

11.8K
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

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

Published on: May 20, 2020

9.3K
Visualizing the Conformational Dynamics of Membrane Receptors Using Single-Molecule FRET
10:59

Visualizing the Conformational Dynamics of Membrane Receptors Using Single-Molecule FRET

Published on: August 17, 2022

3.8K

Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Biophysics

Background:

  • Accurate conformational sampling is crucial for understanding molecular behavior.
  • Traditional molecular dynamics (MD) can be computationally expensive for complex systems.
  • Estimating canonical distribution functions along reaction coordinates presents challenges.

Purpose of the Study:

  • To introduce an enhanced conformational sampling method, virtual-system coupled canonical molecular dynamics (VcMD).
  • To improve the efficiency and applicability of molecular dynamics simulations.
  • To validate VcMD against conventional methods for peptide systems.

Main Methods:

  • Development of VcMD, coupling a virtual system with the molecular system to enhance sampling.
  • Application of VcMD to a two-peptide system in explicit solvent.
  • Comparison with conventional MD and adaptive umbrella sampling simulations.

Main Results:

  • VcMD successfully enhances sampling along a reaction coordinate without canonical distribution estimation.
  • Free-energy landscapes from VcMD, conventional MD, and umbrella sampling showed good convergence.
  • VcMD demonstrated faster peptide association/dissociation dynamics compared to conventional MD.

Conclusions:

  • VcMD is a computationally efficient and methodologically simple approach for enhanced conformational sampling.
  • The method is applicable to complex molecular systems, offering faster dynamics exploration.
  • VcMD provides a valuable alternative for simulating molecular interactions and conformational changes.