Molecular dynamics simulations through GPU video games technologies

Styliani Loukatou, Louis Papageorgiou, Paraskevas Fakourelis, Arianna Filntisi, Eleftheria Polychronidou, Ioannis Bassis, Vasileios Megalooikonomou, Wojciech Makalowski, Dimitrios Vlachakis, Sophia Kossida
Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece
Journal of Molecular Biochemistry 3, 64-71, 2014


   title={Molecular dynamics simulations through GPU video games technologies},

   author={Loukatou, Styliani and Papageorgiou, Louis and Fakourelis, Paraskevas and Filntisi, Arianna and Polychronidou, Eleftheria and Bassis, Ioannis and Megalooikonomou, Vasileios and Maka{l}owski, Wojciech and Vlachakis, Dimitrios and Kossida, Sophia},

   journal={Journal of Molecular Biochemistry},





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Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations.
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