AMBER

swMATH1333MaRDI QIDQ14073FDOQ14073

Author name not available (Why is that?)

Official website: http://ambermd.org

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 (only showing first 100 items - show all)

• 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
• Visualising business processes
• Accelerating Molecular Dynamics Simulations on PlayStation 3 Platform Using Virtual-GRAPE Programming Model
• Low‐Resolution Molecular Dynamics Simulations of the 30S Ribosomal Subunit
• OpenMolcas
• An improved thermal model for SPH metal cutting simulations on GPU
• Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site
• Predicting the efficiency of UAG translational stop signal through studies of physicochemical properties of its composite mono- and dinucleotides
• A model for short \(\alpha\)-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica: Comparison with long-chain \(\alpha\)-neurotoxins and \(\alpha\)-conotoxins
• Scientific computing and algorithms in industrial simulations. Projects and products of Fraunhofer SCAI
• Efficient communication and collection with compact normal forms
• The Sigma MD programm and a generic interface applicable to multi-functional programs with complex, hierarchical command structure
• The value of knowing that you do not know
• Principal nested shape space analysis of molecular dynamics data
• Approximate Counting with Deterministic Guarantees for Affinity Computation
• The Java environment for nature-inspired approaches (JENA): a workbench for biocomputing and biomodelling enthusiasts
• Molecular dynamics simulations study of influence of Tyr422Ala mutation on transcriptional enhancer activation domain 4 (TEAD4) and transcription co-activators complexes
• Quantum Mechanics/Classical Mechanics Modeling of Biological Systems
• Investigating protein-protein and protein-ligand interactions by molecular dynamics simula\-tions
• 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
• Parallel molecular dynamics with irregular domain decomposition
• Spectral accuracy in fast Ewald-based methods for particle simulations
• Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules
• Nonlinear multiscale modeling of polymer materials
• Statistical shape analysis. With applications in R
• Efficient implementation of the many-body reactive bond order (REBO) potential on GPU
• Title not available (Why is that?)
• 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
• Adaptive thermostats for noisy gradient systems
• Force Field Modelling of Conformational Energies
• GPAMM
• IMD
• Title not available (Why is that?)
• GAMESS
• NAMD
• Gromacs
• TINKER
• WebMO
• CHARMM
• LAMMPS
• CPMD
• DESMOND
• PLUMED
• AdResS
• DesParO
• MIBPB
• MorphoJ
• DL_POLY
• DL_POLY_3
• NAMD2
• BALL
• Qmd-plot
• BioSPI
• SAMG
• PDB2PQR
• PAST
• shapes
• CP2K
• MINT
• VARNA
• geomorph
• MYNTS
• HOOMD-blue
• PuReMD
• GROW
• LAMA
• VMD
• OpenMM
• RUMD
• DynamO
• TREMOLO-X
• WHAM
• ACEMD
• Osprey
• DelEnsembleElec
• AutoNester
• ChemoCR
• LC-GAP
• ModelCompare
• ms2
• PackAssistant
• ProMiner
• Simit
• JENA
• MetaPlab
• RASPA
• MDSimAid
• ORCA
• SCOWLP
• DL_MONTE
• dlmontepython
• A new numerical method for nonlocal electrostatics in biomolecular simulations
• An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations
• Multiscale molecular dynamics using the matched interface and boundary method

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