AMBER

swMATH1333MaRDI QIDQ14073FDOQ14073

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Described by source

• AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Cited In (47)

• Classical investigation of long-range coherence in biological systems
• Liouville-type equations for the n-particle distribution functions of an open system
• Modern methods and software systems of molecular modeling and application of behavior algebra
• Quantum dynamics in continuum for proton transport. II: Variational solvent-solute interface
• The adaptive MSINR algorithm to improve error rate for channel equalization
• Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics
• Visualising business processes
• Accelerating Molecular Dynamics Simulations on PlayStation 3 Platform Using Virtual-GRAPE Programming Model
• Spectral accuracy in fast Ewald-based methods for particle simulations
• Scientific Computing and Algorithms in Industrial Simulations
• Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules
• Low‐Resolution Molecular Dynamics Simulations of the 30S Ribosomal Subunit
• Nonlinear multiscale modeling of polymer materials
• An improved thermal model for SPH metal cutting simulations on GPU
• Statistical shape analysis. With applications in R
• Efficient implementation of the many-body reactive bond order (REBO) potential on GPU
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• Massively parallel Monte Carlo for many-particle simulations on GPUs
• Free energy analysis of protein-DNA binding: The EcoRI endonuclease-DNA complex
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi
• Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site
• Adaptive thermostats for noisy gradient systems
• Predicting the efficiency of UAG translational stop signal through studies of physicochemical properties of its composite mono- and dinucleotides
• Force Field Modelling of Conformational Energies
• A model for short \(\alpha\)-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica: Comparison with long-chain \(\alpha\)-neurotoxins and \(\alpha\)-conotoxins
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• A new numerical method for nonlocal electrostatics in biomolecular simulations
• Efficient communication and collection with compact normal forms
• An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations
• Title not available (Why is that?)
• Parallel Molecular Dynamics with Irregular Domain Decomposition
• Multiscale molecular dynamics using the matched interface and boundary method
• Principal nested shape space analysis of molecular dynamics data
• Substructured molecular dynamics using multibody dynamics algorithms
• Fractional Poisson-Nernst-Planck model for ion channels. I: Basic formulations and algorithms
• Approximate Counting with Deterministic Guarantees for Affinity Computation
• Time-dependent density functional theory
• The General Utility Lattice Program (<scp>GULP</scp>)
• The Java environment for nature-inspired approaches (JENA): a workbench for biocomputing and biomodelling enthusiasts
• A GPU-based large-scale Monte Carlo simulation method for systems with long-range interactions
• Molecular dynamics simulations study of influence of Tyr422Ala mutation on transcriptional enhancer activation domain 4 (TEAD4) and transcription co-activators complexes
• Multiresolution molecular mechanics: adaptive analysis
• Quantum Mechanics/Classical Mechanics Modeling of Biological Systems

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