Name
Title | ||
|---|---|---|
Accelerating Molecular Structure Determination Based on Inter-atomic Distances Using OpenCL |
Abstract | ||
|---|---|---|
Fast and accurate determination of the 3D structure of molecules is essential for better understanding their physical, chemical, and biological properties. We focus on an existing method for molecular structure determination: Restrained Molecular Dynamics with Simulated Annealing. In this method a hybrid function, composed by a physical model and experimental restraints, is minimized by simulated annealing. Our goal is to accelerate computation time using commodity multi-core CPUs and GPUs in a heterogeneous computing model. We present a parallel and portable OpenCL implementation of this method. Experimental results are discussed in terms of accuracy, execution time, and parallel scalability. With respect to the XPLOR-NIH professional software package, compared to the single CPU core implementation, we obtain speedups of three to five times (increasing with problem size) on commodity GPUs. We achieve these performances by writing specialized kernels for different problem sizes and hardware architectures. |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1109/TPDS.2014.2385712 | IEEE Transactions on Parallel and Distributed Systems |
Keywords | Field | DocType |
gpu,nmr,opencl,molecular dynamics,molecular structure determination,parallel algorithms,simulated annealing,computational modeling,molecular imaging,nuclear magnetic resonance,proteins | Simulated annealing,Parallel algorithm,Computer science,Parallel computing,Symmetric multiprocessor system,Software,Computational science,Multi-core processor,Piecewise,Computation,Scalability | Journal |
Volume | Issue | ISSN |
PP | 99 | 1045-9219 |
Citations | PageRank | References |
0 | 0.34 | 14 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| István Lorentz | 1 | 0 | 0.34 |
| Razvan Andonie | 2 | 117 | 17.71 |
| Levente Fabry-asztalos | 3 | 20 | 3.21 |