This title appears in the Scientific Report :
2011
Please use the identifier:
http://dx.doi.org/10.1016/j.cpc.2011.04.012 in citations.
Massively parallelized replica-exchange simulations of polymers in GPUs
Massively parallelized replica-exchange simulations of polymers in GPUs
We discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers. Since the sampling of a large ensemble of conformations is a prerequisite for the precise e...
| Personal Name(s): | Groß, J. |
|---|---|
| Janke, W. / Bachmann, M. | |
| Contributing Institute: |
Theorie der Weichen Materie und Biophysik; ICS-2 |
| Published in: | Computer physics communications, 182 (2011) S. 1638 - 1644 |
| Imprint: |
Amsterdam
North Holland Publ. Co.
2011
|
| Physical Description: |
1638 - 1644 |
| DOI: |
10.1016/j.cpc.2011.04.012 |
| Document Type: |
Journal Article |
| Research Program: |
BioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung |
| Series Title: |
Computer Physics Communications
182 |
| Subject (ZB): | |
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| 520 | |a We discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers. Since the sampling of a large ensemble of conformations is a prerequisite for the precise estimation of statistical quantities such as typical indicators for conformational transitions like the peak structure of the specific heat, the advantage of a strong increase in performance of Monte Carlo simulations cannot be overestimated. Employing multithreading and utilizing the massive power of the large number of cores on GPUs, being available in modern but standard graphics cards, we find a rapid increase in efficiency when porting parts of the code from the central processing unit (CPU) to the CPU. (C) 2011 Elsevier B.V. All rights reserved. | ||
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| 500 | |a We acknowledge support by the German-Israeli program "Umbrella" under Grant No. HPC_2, the German Research Foundation (DFG) under Grant Nos. JA 483/24-2/3, the Leipzig Graduate School of Excellence "BuildMoNa", the German-French DFH-UFA PhD College under Grant No. CDFA-02-07, and by the Forschungszentrum Julich for supercomputing time grants jiff39 and jiff43. | ||
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