New software allows simulation of molecular dynamics in large systems

 molecular dynamics simulation
Image: T. Mori (Theoretical Molecular Science Laboratory)
This software promises to open a new era in computational biophysics and biochemistry by allowing scientists to make connections between molecular and cellular-level understanding and to integrate experimental knowledge with theoretical and computational insights.

Although other programs are now available that can perform MD simulations of biomolecules such as proteins, DNA, membranes, and oligosaccharides, a key advantage of GENESIS is its superior computational efficiency on massively parallel supercomputers like the K computer. Using GENESIS, more than ten thousand CPUs can be used in parallel without any reduction in the computational efficiency. This has been achieved thanks to the developments of several new algorithms, including the inverse lookup table, a new domain decomposition scheme, and the use of hybrid (OpenMP + MPI) parallelization.

In the first molecular dynamics simulation, performed by researchers at Harvard University in 1977, protein dynamics were simulated in vacuum conditions. Beginning in the 1990s, simulations of molecules in water or a lipid bilayer have been possible due to advances in MD algorithms and improvements in computer performance. To investigate biomolecular dynamics and function within more realistic cellular environments, much larger biological systems need to be simulated in milli- or microsecond time scales. GENESIS has the potential to be a good computational platform in this context, as it will help to break down the current limitations facing biological MD simulations in terms of size and time.

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