Abstract:

Molecular dynamics is one important area of high performance computing applications.Lots of high performance computing resources or computing cycles are allocated to molecular dynamics simulations.The computing methods and features of molecular dynamics,including commonly used parallel algorithms and performance improvement approaches,are described. Several most often used massively parallel simulation softwares in molecular dynamics and their features are introduced. Finally, the developments and challenges of molecular dynamics simulations are viewed.        

Key words: high performance computing application;molecular dynamics;computational biology