Towards Low Cost Virtual Biological Laboratories: Molecular Modelling Simulation on Commodity Hardware.

Abstract

Many essential cell processes, such as the conformation of embedded proteins, membrane permeability, interaction with drugs and signalling, are directly connected to the molecular dynamics of cell membranes. The importance of this biology has led to an intensifying demand for hardware and software optimized models and tools, implemented on commodity high performance low-cost hardware, in order to provide the scientific community with virtual low cost laboratories. In the light of these considerations, we implemented an accelerated version of a molecular dynamics coarse-grain lipid bilayers simulator on commodity Graphic Processing Units (GPU) architectures. The characteristics of this molecular dynamics model, such as new force fields for pair potentials that include an unconventional representation for water and charges, were particularly challenging. We introduced new algorithms and data structures required by coarse-grain models compared to atomistic ones, for the modelling of the integration timestep, neighbour list generation, and nonbonded force interactions. We characterized the impact on performance of biological systems of differing complexity in terms of size, particle type and timestep. We also compared the simulations of many particle-type systems against single particle-type systems, to evaluate the overhead of additional structures needed to model more complex molecules. Moreover, we performed a detailed analysis on the profiling of the simulation code and its execution flows due to the computation of the non-bonded forces. Finally, we characterized the acceleration and accuracy of the simulations on three GPUs having different computation capabilities and parallelism, achieving one order of magnitude faster simulation execution times