AMBER

swMATH1333MaRDI QIDQ14073

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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

Related Items (47)

Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface ⋮ Unnamed Item ⋮ Nonlinear multiscale modeling of polymer materials ⋮ The General Utility Lattice Program (<scp>GULP</scp>) ⋮ Massively parallel Monte Carlo for many-particle simulations on GPUs ⋮ An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations ⋮ Unnamed Item ⋮ Molecular dynamics simulations study of influence of Tyr422Ala mutation on transcriptional enhancer activation domain 4 (TEAD4) and transcription co-activators complexes ⋮ Parallel Molecular Dynamics with Irregular Domain Decomposition ⋮ DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi ⋮ Multiresolution molecular mechanics: adaptive analysis ⋮ Substructured molecular dynamics using multibody dynamics algorithms ⋮ Multiscale molecular dynamics using the matched interface and boundary method ⋮ A GPU-based large-scale Monte Carlo simulation method for systems with long-range interactions ⋮ Fractional Poisson-Nernst-Planck model for ion channels. I: Basic formulations and algorithms ⋮ Approximate Counting with Deterministic Guarantees for Affinity Computation ⋮ Spectral accuracy in fast Ewald-based methods for particle simulations ⋮ Classical investigation of long-range coherence in biological systems ⋮ Visualising business processes ⋮ The Java environment for nature-inspired approaches (JENA): a workbench for biocomputing and biomodelling enthusiasts ⋮ Efficient communication and collection with compact normal forms ⋮ A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver ⋮ Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics ⋮ Unnamed Item ⋮ Liouville-type equations for the n-particle distribution functions of an open system ⋮ Unnamed Item ⋮ An improved thermal model for SPH metal cutting simulations on GPU ⋮ Force Field Modelling of Conformational Energies ⋮ Unnamed Item ⋮ A new numerical method for nonlocal electrostatics in biomolecular simulations ⋮ Predicting the efficiency of UAG translational stop signal through studies of physicochemical properties of its composite mono- and dinucleotides ⋮ Low‐Resolution Molecular Dynamics Simulations of the 30S Ribosomal Subunit ⋮ A model for short \(\alpha\)-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica: Comparison with long-chain \(\alpha\)-neurotoxins and \(\alpha\)-conotoxins ⋮ Time-dependent density functional theory ⋮ Adaptive Thermostats for Noisy Gradient Systems ⋮ Efficient implementation of the many-body reactive bond order (REBO) potential on GPU ⋮ Quantum Mechanics/Classical Mechanics Modeling of Biological Systems ⋮ Principal nested shape space analysis of molecular dynamics data ⋮ Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site ⋮ Unnamed Item ⋮ Scientific Computing and Algorithms in Industrial Simulations ⋮ Statistical Shape Analysis, with Applications in R ⋮ The adaptive MSINR algorithm to improve error rate for channel equalization ⋮ Accelerating Molecular Dynamics Simulations on PlayStation 3 Platform Using Virtual-GRAPE Programming Model ⋮ Free energy analysis of protein-DNA binding: The EcoRI endonuclease-DNA complex ⋮ Modern methods and software systems of molecular modeling and application of behavior algebra ⋮ Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules

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