This article was published online on 17 July 2013. The article was subsequently amended in order to acknowledge the original occurrence of a specific technique employed by the authors. This notice is included in the online and print versions to indicate that both have been corrected 3 September 2013.
GPU-accelerated molecular mechanics computations
Article first published online: 17 JUL 2013
Copyright © 2013 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 34, Issue 26, pages 2249–2260, 5 October 2013
How to Cite
How to cite this article: J. Comput. Chem. 2013, 34, 2249–2260. DOI: 10.1002/jcc.23384, , .
- Issue published online: 5 SEP 2013
- Article first published online: 17 JUL 2013
- Manuscript Accepted: 20 JUN 2013
- Manuscript Revised: 19 JUN 2013
- Manuscript Received: 11 FEB 2013
- molecular mechanics;
- cell lists;
In this article, we describe an improved cell-list approach designed to match the Kepler architecture of General-purpose graphics processing units (GPGPU). We explain how our approach improves load balancing for the above algorithm and how warp intrinsics are used to implement Newton's third law for the nonbonded force calculations. We also talk through our approach to exclusions handling together with a method to calculate bonded forces and 1–4 electrostatic scaling using a single Cuda kernel. Performance benchmarks are included in the last sections to show the linear scaling of our implementation using a step minimization method. In addition, multiple performance benchmarks demonstrate the contribution of various optimizations we used for our implementations. © 2013 Wiley Periodicals, Inc.