Paper Citing NAMD - Abstract
LeBard, David N.
Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware
MOLECULAR SIMULATION, 40:802-820, 2014
The timescales of biological processes, primarily those inherent to the molecular mechanisms of disease, are long (> mu s) and involve complex interactions of systems consisting of many atoms (>10(6)). Simulating these systems requires an advanced computational approach, and as such, coarse-grained (CG) models have been developed and highly optimised for accelerator hardware, primarily graphics processing units (GPUs). In this review, I discuss the implementation of CG models for biologically relevant systems, and show how such models can be optimised and perform well on GPU-accelerated hardware. Several examples of GPU implementations of CG models for both molecular dynamics and Monte Carlo simulations on purely GPU and hybrid CPU/GPU architectures are presented. Both the hardware and algorithmic limitations of various models, which depend greatly on the application of interest, are discussed.
