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

Force On A Current Loop In A Magnetic Field01:17

Force On A Current Loop In A Magnetic Field

4.0K
Magnetic forces on wires carrying current are most frequently applied in motors. A DC motor is a device that converts electrical energy into mechanical work. In motors, wire loops are enclosed in a magnetic field. When current flows through the loops, the magnetic field applies torque, which causes the shaft to rotate. The direction of the current is reversed once the loop's surface area is lined up with the magnetic field, causing a constant torque on the loop. During the process, commutators...
4.0K
Intermolecular Forces03:13

Intermolecular Forces

70.2K
Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen...
70.2K
Electromotive Force02:36

Electromotive Force

29.8K
Electricity is generated by either electrons or ions flowing through a solution or a conducting medium. This flow of electrons or specifically electrical charge is defined as an electric current. When electrons move through a wire, they generate an electric current. It can be recalled  that in a redox reaction, electrons are lost and gained. In the spontaneous redox reaction of zinc  with copper, when zinc is immersed in a copper ion solution, a transfer of electrons from one substance to...
29.8K
Intermolecular vs Intramolecular Forces03:00

Intermolecular vs Intramolecular Forces

96.2K
Intermolecular forces (IMF) are electrostatic attractions arising from charge-charge interactions between molecules. The strength of the intermolecular force is influenced by the distance of separation between molecules. The forces significantly affect the interactions in solids and liquids, where the molecules are close together. In gases, IMFs become important only under high-pressure conditions (due to the proximity of gas molecules). Intermolecular forces dictate the physical properties of...
96.2K
Intermolecular Forces in Solutions02:28

Intermolecular Forces in Solutions

38.8K
The formation of a solution is an example of a spontaneous process, a process that occurs under specified conditions without energy from some external source.
When the strengths of the intermolecular forces of attraction between solute and solvent species in a solution are no different than those present in the separated components, the solution is formed with no accompanying energy change. Such a solution is called an ideal solution. A mixture of ideal gases (or gases such as helium and argon,...
38.8K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.5K

You might also read

Related Articles

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

Sort by
Same author

Signatures of Protein Fold Switching in the Unfolded State.

Biophysical journal·2026
Same author

Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs.

bioRxiv : the preprint server for biology·2026
Same author

Time-Resolved Single-Molecule FRET Reveals Length-Dependent Nucleosome Decompaction by Poly(ADP-ribose).

bioRxiv : the preprint server for biology·2026
Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026
Same author

Dynamical Buffering of Reconfiguration Dynamics in Intrinsically Disordered Proteins.

JACS Au·2026
Same author

Free energy of collagen-mimetic peptide dimerization and implications for fibrillization.

Biophysical journal·2026
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jan 21, 2026

Covalent Immobilization of Proteins for the Single Molecule Force Spectroscopy
11:13

Covalent Immobilization of Proteins for the Single Molecule Force Spectroscopy

Published on: August 20, 2018

11.6K

Atomistic Force Fields for Proteins.

Robert B Best1

  • 1Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA. robert.best2@nih.gov.

Methods in Molecular Biology (Clifton, N.J.)
|August 10, 2019
PubMed
Summary
This summary is machine-generated.

Choosing the right protein molecular dynamics (MD) force field is crucial for accurate simulations. This guide overviews historical force field development and offers advice for selecting appropriate models and interpreting results.

Keywords:
AMBERCHARMMConformational changeGROMOSMembrane proteinsOPLSProtein foldingTransferable modelUnfolded state

More Related Videos

Advanced Self-Healing Asphalt Reinforced by Graphene Structures: An Atomistic Insight
08:03

Advanced Self-Healing Asphalt Reinforced by Graphene Structures: An Atomistic Insight

Published on: May 31, 2022

5.6K
Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope
06:45

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Published on: February 28, 2019

9.4K

Related Experiment Videos

Last Updated: Jan 21, 2026

Covalent Immobilization of Proteins for the Single Molecule Force Spectroscopy
11:13

Covalent Immobilization of Proteins for the Single Molecule Force Spectroscopy

Published on: August 20, 2018

11.6K
Advanced Self-Healing Asphalt Reinforced by Graphene Structures: An Atomistic Insight
08:03

Advanced Self-Healing Asphalt Reinforced by Graphene Structures: An Atomistic Insight

Published on: May 31, 2022

5.6K
Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope
06:45

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Published on: February 28, 2019

9.4K

Area of Science:

  • Computational Biology
  • Biophysics
  • Molecular Modeling

Background:

  • All-atom classical force fields are valuable for protein molecular dynamics (MD) simulations, balancing detail with computational feasibility.
  • The extensive history of force field development has resulted in numerous versions, creating challenges for new users in selecting appropriate parameters.
  • Advancements in hardware and enhanced sampling methods now enable the simulation of biologically relevant timescales (microseconds and beyond).

Purpose of the Study:

  • To provide a historical overview of the evolution of protein molecular dynamics force fields.
  • To offer guidance on selecting the most suitable force field for specific computational applications.
  • To suggest strategies for addressing discrepancies between simulation results and experimental data.

Main Methods:

  • Review of historical development and branching of classical force fields for protein simulations.
  • Comparative analysis of force field characteristics and their suitability for different biological systems and timescales.
  • Discussion of methodologies for validating simulation outcomes against experimental evidence.

Main Results:

  • Identification of key historical factors influencing the diversity of current force field models.
  • A framework for systematically evaluating and choosing among available protein force fields.
  • Recommendations for troubleshooting and reconciling simulation-force field inconsistencies with experimental findings.

Conclusions:

  • Understanding the historical context of force fields is essential for informed selection in molecular dynamics.
  • A structured approach to force field selection enhances the reliability and predictive power of protein simulations.
  • Addressing simulation-experiment conflicts requires careful consideration of the chosen force field and simulation parameters.