An overview of the Amber biomolecular simulation package
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Summary
The most recent developments, since version 9 was released in April 2006, of the Amber and AmberTools MD software packages are outlined, referred to here as simply the Amber package.
- Type
- article
- Published
- 2013-03-01
- Cited by
- 2,480
- References
- 97
- OpenAlex
- https://openalex.org/W2103325328
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:18048153
Keywords
Software package, Computer science, Software, Computational science, Operating system
References
- Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm
- The implementation of a fast and accurate QM/MM potential method in Amber
- Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: application to the intramolecular hydrogen transfer in pentadiene.
- NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
- Semiclassical theory of electronically nonadiabatic dynamics: results of a linearized approximation to the initial value representation
- Molecular Mechanical and Molecular Dynamic Simulations of Glycoproteins and Oligosaccharides. 1. GLYCAM_93 Parameter Development
- Quantum diffusion in liquid water from ring polymer molecular dynamics.
- Accelerated Poisson–Boltzmann calculations for static and dynamic systems
- Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
- Comparison of simple potential functions for simulating liquid water
- Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
- Isotropic periodic sum: a method for the calculation of long-range interactions.
- Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium
- Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
- Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids
- Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
- Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.
- Ring polymer molecular dynamics beyond the linear response regime: Excess electron injection and trapping in liquids.
- The formulation of quantum statistical mechanics based on the Feynman path centroid density. IV. Algorithms for centroid molecular dynamics
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
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- Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
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- Consistent approach for calculating protein pKa's using Poisson-Boltzmann Model
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