Category: Physical Science
NVIDIA CUDA Spotlight: GPU-Accelerated Molecular Dynamics
This week’s NVIDIA spotlight is on Dr. Ross Walker, assistant research professor with the San Diego Supercomputer Center (SDSC) at UC San Diego and adjunct assistant professor in the Department of Chemistry and Biochemistry at UC San Diego.
Massively parallelized replica-exchange simulations of polymers on GPUs
Authors discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers.
Toward large-scale Hybrid Monte Carlo simulations of the Hubbard model on graphics processing units
One of the most efficient non-perturbative methods for the calculation of thermal properties of quantum systems is the Hybrid Monte Carlo algorithm, as evidenced by its use in large-scale lattice quantum chromodynamics calculations. The performance of this algorithm is determined by the speed at which the fermion operator is applied to a given vector, as it is the central operation in the preconditioned conjugate gradient iteration.
PSPFFT: Parallel FFT-based Poisson solver for isolated three-dimensional systems
Authors describe an implementation to solve Poisson’s equation for an isolated system on a unigrid mesh using FFTs. The method solves the equation globally on mesh blocks distributed across multiple processes on a distributed-memory parallel computer.
QYMSYM: A GPU-accelerated hybrid symplectic integrator
Authors describe a parallel hybrid symplectic integrator for planetary system integration that runs on a graphics processing unit (GPU). The integrator identifies close approaches between particles and switches from symplectic to Hermite algorithms for particles that require higher resolution integrations
GPU-accelerated atom and dynamic bond visualization using hyperballs
Ray casting on graphics processing units (GPUs) opens new possibilities for molecular visualization. We describe the implementation and calculation of diverse molecular representations such as licorice, ball-and-stick, space-filling van der Waals spheres, and approximated solvent-accessible surfaces using GPUs
Fast calculation of electrostatic potentials on the GPU
Here we study the potential employment of hardware accelerators like the graphics processing unit or the application-specific integrated circuit MD-GRAPE-3 for the purpose of efficient computation of ESPs.
Special issue of Procedia Computer Science highlights GPU developments
The 11th International Conference on Computational Science and Applications (ICCSA 2011) was held on June 20-23, 2011, at the University of Cantabria, Santander, Spain. ICCSA 2011 was the next event in a series of highly successful International Conferences on Computational Science and Its Applications (ICCSA), previously held in Fukuoka, Japan (2010), Suwon, Korea (2009), Perugia, Italy (2008), Kuala…
BD_BOX: Brownian dynamics simulations on CPU and GPU
BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included.
Acceleration of the GAMESS-UK electronic structure package
The approach used to calculate the two-electron integral by many electronic structure packages including generalized atomic and molecular electronic structure system-UK has been designed for CPU-based compute units. We redesigned the two-electron compute algorithm for acceleration on a graphical processing unit (GPU).
