15509

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

David M. Bowman
Centre for Biomedical Research, University of the Algarve
University of the Algarve, 2015

@article{bowman2015optimization,

   title={Optimization of molecular dynamics simulation code and applications to biomolecular systems},

   author={Bowman, David M},

   year={2015}

}

Download Download (PDF)   View View   Source Source   

737

views

The performance of molecular dynamics (MD) software such as GROMACS is limited by the software’s ability to perform force calculations. The largest part of this is for nonbonded interactions such as between water molecules and water molecules and solute. The determination of nonbonded interactions may account for over 90% of the total computation and real time of a simulation. The objective of this project is to greatly improve the performance of force calculations for nonbonded on a single core/processor. By doing this it is possible to raise the bar on all simulations that can be performed by GROMACS (single, multi-core or MPI). The resulting modifications need to then be verified to determine that the software still works. That it is still ‘good enough’ for performing molecular dynamics simulations.
No votes yet.
Please wait...

* * *

* * *

Featured events

2018
November
27-30
Hida Takayama, Japan

The Third International Workshop on GPU Computing and AI (GCA), 2018

2018
September
19-21
Nagoya University, Japan

The 5th International Conference on Power and Energy Systems Engineering (CPESE), 2018

2018
September
22-24
MediaCityUK, Salford Quays, Greater Manchester, England

The 10th International Conference on Information Management and Engineering (ICIME), 2018

2018
August
21-23
No. 1037, Luoyu Road, Hongshan District, Wuhan, China

The 4th International Conference on Control Science and Systems Engineering (ICCSSE), 2018

2018
October
29-31
Nanyang Executive Centre in Nanyang Technological University, Singapore

The 2018 International Conference on Cloud Computing and Internet of Things (CCIOT’18), 2018

HGPU group © 2010-2018 hgpu.org

All rights belong to the respective authors

Contact us: