GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features
By Tai-Sung Lee, D. Cerutti, D. Mermelstein, Charles Lin, S. LeGrand, Timothy J. Giese, Adrian E. Roitberg, David A. Case, Ross C. Walker, D. York. Journal of Chemical Information and Modeling, 2018
423 citations recorded by the source corpus.
We report progress in GPU-accelerated molecular dynamics and free energy methods in Amber18. Of particular interest is the development of alchemical free energy algorithms, including free energy perturbation and thermodynamic integration methods with support for non-linear softcore potential and parameter interpolation transformation pathways. These methods can be used in conjunction with enhanced sampling techniques such as replica exchange, constant pH molecular dynamics and new 12-6-4 potentials for metal ions. Additional performance enhancements have been made that enable appreciable speed-up on GPUs relative to the previous software release.
Subfields: Atomic and Molecular Physics, and Optics, Materials Chemistry
View Paper: https://www.semanticscholar.org/paper/46d3782d6bfbdeefa60ef5881b2b1e763e65e80f
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In Atomic and Molecular Physics, and Optics
In Materials Chemistry
Citations in the corpus
- A fast and high-quality charge model for the next generation general AMBER force field. (2020, methodology): “The thermodynamic integration (TI) modules of both central processing unit (CPU) and graphic processing unit (GPU) versions 67–69 implemented in AMBER18 66 were adopted to carry out simulations and calculate the SFEs.”