Tag: molecular modeling
Parallel verlet neighbor list algorithm for GPU-optimized MD simulations
Computational biophysics research group of Professor Samuel Cho from Wake Forest University developed a novel parallel Verlet neighbor list algorithm for performing coarse-grained MD simulations of biologically relevant systems.
High-Throughput parallel blind Virtual Screening using BINDSURF
Authors present BINDSURF, a novel VS methodology that scans the whole protein surface in order to find new hotspots, where ligands might potentially interact with, and which is implemented in last generation massively parallel GPU hardware, allowing fast processing of large ligand databases.
GPU Linear Algebra Libs and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations
We have developed and implemented new features in the MOPAC2009 program in order to allow it to run faster on GPUs and shared-memory CPUs.
Workshop: Rapid Molecular Dynamics Prototyping and Simulations on GPUs with OpenMM
Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures.
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.
