Scalable molecular dynamics on CPU and GPU architectures with NAMD.
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Summary
The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.
- Type
- article
- Published
- 2020-07-28
- Cited by
- 2,738
- References
- 245
- Access
- Open access
- OpenAlex
- https://openalex.org/W3046751266
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:220978458
Keywords
Computer science, Scalability, Molecular dynamics, Parallel computing, CUDA
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- Modeling Transport Through Synthetic Nanopores
- Statistical Mechanics of Fluid Mixtures
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- Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6
- Finding transition pathways using the string method with swarms of trajectories.
- Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
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- Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories
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- Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics
- MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations.
- Genotype & Phenotype in Lowe Syndrome: Specific OCRL1 patient mutations differentially impact cellular phenotypes
- Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD
- Mechanical Activation of MscL Revealed by a Locally Distributed Tension Molecular Dynamics Approach
- Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d
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