Tag: molecular modeling
Accelerating knowledge-based energy evaluation in protein structure modeling with GPU
We present an efficient implementation of knowledge-based energy functions by taking advantage of the recent Graphics Processing Unit (GPU) architectures
DMD: An Efficient and Versatile Simulation Method for Fine Protein Characterization
We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware.
Electronic Structure Calculation Methods on Accelerators workshop at Oak Ridge
This conference seeks to bring together computationally oriented scientists interested in using accelerator coprocessors in electronic structure theory. We will discuss recent advances, barriers and perspectives in modeling electronic structure on accelerators.
Call For Papers: High Performance Simulation of biological systems
The goal of this track is to explore the use of emerging parallel computing architectures as well as High Performance Computing systems (Supercomputers, Clusters, Grids) for the simulation of relevant biological systems.
VPAC – Drug Docking and Modeling Ligands Interactions Based on NAMD
Using NVIDIA Tesla GPU technology, researchers can routinely simulate protein molecules in the order of hundreds of nanoseconds. At this timescale, it is possible to investigate detailed interactions of ligands with receptors starting with free ligand in a solution.
GPU-accelerated high-accuracy molecular docking using guided differential evolution
We have presented methods for parallelising flexible molecular docking with MolDock on both CPUs and CUDA enabled GPUs which are applicable to other common flexible molecular docking methods.
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
In this work authors present a kinetic model for the binding process of serine protease β-trypsin inhibitor benzamidine obtained from extensive high-throughput all-atom MD simulations of free ligand binding using the ACEMD (GPU accelerated biomolecular dynamics) software on the GPUGRID.net distributed computing network.
Copernicus: a new paradigm for parallel adaptive molecular dynamics
We have shown that the Copernicus framework effectively increases the scale at which biomolecular molecular dynamics simulations can be performed from a few hundred cores to many thousands and beyond, likely reaching millions of cores for large molecules.
Webinar: GPU-enabled Macromolecular Simulation. Challenges and Opportunities
In this webinar, Michela Taufer, Assistant Professor, University of Delaware, discusses various key aspects of simulation methodologies of macro molecular systems specifically adapted to GPUs. She will also visit some of the underlying challenges and solutions devised to tackle them.
Call for Paper: Quantum Mechanical Foundations of Multiscale Modeling
This special issue will focus on the development of efficient QM methods that are applicable to large-scale calculations of materials on the order of several thousand atoms or more. Manuscripts detailing theoretical constructs, algorithmic advances, or software designs are welcome.
