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

Mass Analyzers: Overview01:13

Mass Analyzers: Overview

700
The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
700
Ammeter01:11

Ammeter

2.2K
An ammeter is a current measuring instrument. In the circuit, it is represented by the symbol A. The ammeter is placed in series with the device or component to measure the current. A series connection is used because objects in series have the same current passing through them. If a circuit has multiple resistors and the current needs to be measured in each resistor, the number of ammeters required depends on whether the circuit is in series or parallel.
When an ammeter is used to measure the...
2.2K
Mass Analyzers: Common Types01:19

Mass Analyzers: Common Types

628
The quadrupole mass analyzer consists of four cylindrical metal rods arranged in a diamond carrying a DC voltage and a radio-frequency AC voltage. The motion of ions through the quadrupole depends on the field strength, causing only ions of a certain m/z to resonate successfully and strike the detector at a given field strength. Though the transmission rate for these analyzers is high, the exact elemental composition of the sample is not determined because of low resolution; however, they are...
628
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

1.1K
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.
Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called collision-induced...
1.1K
Beams with Unsymmetric Loadings01:17

Beams with Unsymmetric Loadings

124
Analyzing a supported beam under unsymmetrical loadings is essential in structural engineering to understand how beams respond to varied force distributions. This analysis involves calculating the deflection and identifying points where the slope of the beam is zero, which are crucial for ensuring structural stability and functionality.
The first moment-area theorem determines the slope at any point on the beam. This theorem indicates that the change in slope between two points on a beam...
124
Amplifying Signals via Enzymatic Cascade01:22

Amplifying Signals via Enzymatic Cascade

8.5K
When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze...
8.5K

You might also read

Related Articles

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

Sort by
Same author

Quantum-Centric Alchemical Free Energy Calculations.

Journal of chemical theory and computation·2026
Same author

Beyond Single Structures: The Role of Structural Ensembles in Discrete-Continuum Modeling of Highly Charged Metal Ions.

Journal of chemical theory and computation·2026
Same author

IID-KG: An ontology-aligned literature-derived knowledge graph for infectious and immune-mediated diseases.

bioRxiv : the preprint server for biology·2026
Same author

Molecular Quantum Computations on a Protein.

Journal of chemical theory and computation·2026
Same author

Advancing Reproducibility and Open Data in Theoretical and Computational Chemistry.

Journal of chemical theory and computation·2026
Same author

Development of an optimized parameter set for monovalent ions in the reference interaction site model of solvation.

The Journal of chemical physics·2026
Same journal

PACEff Builder: An Efficient Platform for Constructing PACE Hybrid-Resolution Models for Molecular Dynamics Simulations of Aqueous Protein, Peptide Assembly, and Membrane Protein Systems.

Journal of chemical information and modeling·2026
Same journal

TransKla: A Local-Global Cross-Attention Based Transformer Approach for Prediction of Lysine Lactylation Sites.

Journal of chemical information and modeling·2026
Same journal

CondenSimAdapter: A Versatile Builder for Multiscale Simulations of Protein Condensates with Broad Force-Field Compatibility and Robust Dense-Phase Relaxation.

Journal of chemical information and modeling·2026
Same journal

Simulation Guided Design of a Potentially Hyperactive Ice Nucleating Protein.

Journal of chemical information and modeling·2026
Same journal

Setting the Bases of the Photogenotoxicity of <i>p</i>-Aminobenzoic Acid.

Journal of chemical information and modeling·2026
Same journal

Probing Charge-Controlled Inter-Domain Flexibility: Integrating Experimental and Coarse-Grained Approaches.

Journal of chemical information and modeling·2026
See all related articles

Related Experiment Video

Updated: Jul 14, 2025

JenaTron - An Experimental Approach to Study the Effects of Plant History and Soil History on Grassland Ecosystem Functioning
09:23

JenaTron - An Experimental Approach to Study the Effects of Plant History and Soil History on Grassland Ecosystem Functioning

Published on: March 21, 2025

983

AmberTools.

David A Case1, Hasan Metin Aktulga2, Kellon Belfon3

  • 1Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States.

Journal of Chemical Information and Modeling
|October 8, 2023
PubMed
Summary
This summary is machine-generated.

AmberTools23 offers new features for molecular simulations. This free, open-source software aids in setting up, running, and analyzing simulations.

More Related Videos

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments
20:28

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

Published on: October 2, 2012

14.2K
Non-invasive Assessments of Subjective and Objective Recovery Characteristics Following an Exhaustive Jump Protocol
08:21

Non-invasive Assessments of Subjective and Objective Recovery Characteristics Following an Exhaustive Jump Protocol

Published on: June 8, 2017

7.8K

Related Experiment Videos

Last Updated: Jul 14, 2025

JenaTron - An Experimental Approach to Study the Effects of Plant History and Soil History on Grassland Ecosystem Functioning
09:23

JenaTron - An Experimental Approach to Study the Effects of Plant History and Soil History on Grassland Ecosystem Functioning

Published on: March 21, 2025

983
A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments
20:28

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

Published on: October 2, 2012

14.2K
Non-invasive Assessments of Subjective and Objective Recovery Characteristics Following an Exhaustive Jump Protocol
08:21

Non-invasive Assessments of Subjective and Objective Recovery Characteristics Following an Exhaustive Jump Protocol

Published on: June 8, 2017

7.8K

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Biophysics

Background:

  • Molecular simulations are crucial for understanding molecular behavior.
  • AmberTools is a widely used suite for molecular simulations.
  • Continuous development is needed to enhance simulation capabilities.

Purpose of the Study:

  • To introduce the new features in AmberTools23.
  • To provide a concise overview of updates for researchers.
  • To highlight improvements in molecular simulation analysis.

Main Methods:

  • Description of new functionalities in AmberTools23.
  • Review of software enhancements.
  • Application note format for clear communication.

Main Results:

  • AmberTools23 includes updated tools for simulation setup.
  • New features facilitate enhanced analysis of simulation data.
  • The release offers improved performance and usability.

Conclusions:

  • AmberTools23 represents a significant advancement in molecular simulation software.
  • The new features empower researchers with more powerful tools.
  • Open-source accessibility ensures broad adoption and contribution.