AmberTools

David A Case1, Hasan Metin Aktulga2, Kellon Belfon3

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

Summary

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

Related Concept Videos

Mass Analyzers: Overview01:13

Mass Analyzers: Overview

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...
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Ammeter01:11

Ammeter

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...
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Mass Analyzers: Common Types01:19

Mass Analyzers: Common Types

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...
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Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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...
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Beams with Unsymmetric Loadings01:17

Beams with Unsymmetric Loadings

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...
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Amplifying Signals via Enzymatic Cascade01:22

Amplifying Signals via Enzymatic Cascade

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...
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