TY - JOUR
T1 - Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation?
AU - Biagini, Tommaso
AU - Petrizzelli, Francesco
AU - Truglio, Mauro
AU - Cespa, Roberto
AU - Barbieri, Alessandro
AU - Capocefalo, Daniele
AU - Castellana, Stefano
AU - Tevy, Maria Florencia
AU - Carella, Massimo
AU - Mazza, Tommaso
PY - 2019/5/1
Y1 - 2019/5/1
N2 - In several fields of research, molecular dynamics simulation techniques are exploited to evaluate the temporal motion of particles constituting water, ions, small molecules, macromolecules, or more complex systems over time. These techniques are considered difficult to setup, computationally demanding and require high specialization and scientific skills. Moreover, they need specialized computing infrastructures to run faster and make the simulation of big systems feasible. Here, we have simulated 3 systems of increasing sizes on scientific- and gaming-enabled graphic processing unit (GPU) cards with Amber, GROMACS, and NAMD and measured their performance accounting also for the market prices of the GPU cards where they were run on.
AB - In several fields of research, molecular dynamics simulation techniques are exploited to evaluate the temporal motion of particles constituting water, ions, small molecules, macromolecules, or more complex systems over time. These techniques are considered difficult to setup, computationally demanding and require high specialization and scientific skills. Moreover, they need specialized computing infrastructures to run faster and make the simulation of big systems feasible. Here, we have simulated 3 systems of increasing sizes on scientific- and gaming-enabled graphic processing unit (GPU) cards with Amber, GROMACS, and NAMD and measured their performance accounting also for the market prices of the GPU cards where they were run on.
KW - GPU computing
KW - molecular dynamics simulation
KW - protein structure
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U2 - 10.1177/1176934319850144
DO - 10.1177/1176934319850144
M3 - Comment/debate
AN - SCOPUS:85071287927
VL - 15
JO - Evolutionary Bioinformatics
JF - Evolutionary Bioinformatics
SN - 1176-9343
ER -