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Amber Molecular Dynamics

Amber 2024

BIOMOLECULAR SIMULATION TOOL

AMBER is a key application in Molecular Dynamics used to simulate biocatalysis and the interaction between drug candidates and protein receptors. At the begining, it was a program designed to do Assisted Model Building with Energy Refinement and now is a suite which provides a set of biomolecular simulation tools to apply the AMBER force fields. Released in april 2024, AMBER 24 and AmberTools 224are still the best software packages for Molecular Dynamics.
 
 An exemplary feature of AMBER is the ability to use NVIDIA GPUs to massively accelerate complex molecular simulations. This enhances sampling efficiency, improves research accuracy, enables more advanced science and speeds up the research process.

License fees for Amber24 will change on April 15, 2023. The fee for not-for-profit users will be removed, and fees for for-profit users will become $25,000 USD for new licensees, and $20,000 for returning sites.

AMBER CERTIFIED MD SYSTEMS

As the sole provider of AMBER Certified MD Systems in Europe, LinuxVixion offer turnkey solutions in collaboration with key AMBER developer Professor Ross Walker to offer value-add systems for GPU accelerated Molecular Dynamics simulations.

The Amber22 package builds on AmberTools22 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides (much) better performance on multiple CPUs, and dramatic speed improvements on GPUs.

Save time installing, optimizing, benchmarking and validating and do more science instead.

Amber Molecular Dynamics

Image: A pseudotrajectory of the homodecameric human glutamine synthetase.

Benedikt Frieg and Holger Gohlke (FZJ Jülich)

Overview of AmberTools24

AmberTools24 (released on April 30, 2024) consists of the following major codes:

 

 

nabc/sff: tools to build molecules, run MD or apply restraints using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models.

antechamber and MCPB.py: programs to create force fields for general organic molecules and metal centers.

tleap and parmed: basic preparatory tools for Amber simulations

sqm and Quick: semiempirical, DFTB, and ab initio quantum chemistry codes, for stand-alone calculations or in QM/MM

pbsa: performs numerical solutions to Poisson-Boltzmann models

3D-RISM: solves integral equation models for solvation

sander: workhorse program for molecular dynamics simulations

gem.pmemd: tools for using advanced force fields

mdgx: a program for pushing the boundaries of Amber MD, primarily through parameter fitting. Also includes customizable virtual sites and explicit solvent MD capabilities.

cpptraj and pytraj: tools for analyzing structure and dynamics in trajectories

MMPBSA.py: energy-based analyses of MD trajectories

fe-toolkit: routines to analyze alchemical free energy simulations

Among the New Features (more coming soon):

 

New and updated forcefields:

 

Inclusion of the ABCG2 charge model for GAFF2

 

Quick package for Hartree-Fock and DFT electronic stucture calculations, with GPU support. Quick is integrated into sander for QM/MM simulations, and AmberTools24 contains significant performance improvements, a new geometry optimizer, and support for spin-unrestricted calculations.

 

Detailed changelog for cpptraj. Changes include GIST improvements, new cluster analysis, and a “prepareforleap” script with support for carbohydrates.

 

fe-toolkit package of routines to analyze alchemical free energy calculations.

 

If you want the fastest AMBER Molecular Dynamics solution on desktop hardware, take a look at our specialized GPU supercomputers

CERTIFIED SYSTEMS

Our GPU Workstations and Servers are certified. All NVidia GeForce systems are fully validated for numerical correctness using custom validation suites.

GPU computing

«I personally verify all LinuxVixion machines»

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