Site Announcements

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May 13-14, 2012  |  San Jose, CA

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May 14-17, 2012  |  San Jose, CA
   
  • Innovative Parallel Computing / Foundations & Applications of GPU, Manycore, and Heterogeneous Systems (INPAR’12) is a new academic conference which is co-located with NVidia's GPU Technology Conference. Click here for the full Call for Papers.

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Molecular Modeling

Welcome to the Molecular Modeling community.

This community covers the full range of molecular modeling applications on GPUs.  I invite group members to post links to recent publications, links to calls for participation for journals and conferences, and exchange example codes and ideas for GPU algorithms.  I would especially like to maintain a bibliography of research papers on the use of GPUs in the many branches of molecular modeling, and would encourage others to contribute to the list of GPU papers that I've already started here.

John E. Stone, University of Illinois at Urbana-Champaign

Julie Mitchell, University of Wisconsin-Madison

Featured Events

High Performance Simulation of Biological systems at MAS 2012

 Call For Papers

 

High Performance Simulation of biological systems 

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Featured Stories and Papers

Molecular Docking on FPGA and GPU Platforms (IEEE)

Abstract:
Molecular docking is an important problem of bioinformatics aiming at the prediction of binding poses of molecules. Auto Dock is a popular, open-source docking software applying a computationally expensive but parallelizable algorithm. This paper introduces an FPGA-based and a GPU-based implementation of Auto Dock and shows how the original algorithm can be effectively accelerated on the two different platforms. According to test runs, both implementations achieve significant speedups over Auto Dock running on a single CPU core and on a quad-core system. Comparison of the two implementations proves that many-core graphics processing units can be a real alternative to FPGAs in the field of high performance computing.

Paper available at IEEE.

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FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME (IEEE)

Abstract:

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Exploring Fine-Grained Task-Based Execution on Multi-GPU Systems (IEEE)

Abstract

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Loose Capacity-Constrained Representatives for the Qualitative Visual Analysis in Molecular Dynamics (ACM)

Abstract:

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High-performance Blob-based iterative reconstruction of electron tomography on multi-GPUs (ACM)

Three-dimensional (3D) reconstruction of electron tomography (ET) has emerged as a leading technique to elucidate the molecular structures of complex biological specimens. Blob-based iterative methods are advantageous reconstruction methods for 3D reconstruction of ET, but demand huge computational costs. Multiple Graphic processing units (multi-GPUs) offer an affordable platform to meet these demands, nevertheless, are not efficiently used owing to a synchronous communication scheme and the limited available memory of GPUs. We propose a multilevel parallel scheme combined with an asynchronous communication scheme and a blob-ELLR data structure. The asynchronous communication scheme is used to minimize the idle GPU time.

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GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution: Real World Applications (ACM)

Abstract:

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New CUDA Toolkit Released

A new production release of CUDA shipped today. This new release makes it faster and easier to accelerate scientific research with GPUs.  Key features include a re-designed Visual Profiler with automated performance analysis, a new LLVM-based compiler that helps your apps run up to 10% faster, and 1000+ new imaging and signal processing functions in the NPP library.  We’ve also added a new tri-diagonal solver, 2x faster SpMV using the ELL hybrid format, and some great improvements to the debugging and performance analysis tools.  Learn more and download from CUDAZone

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Featured Forum Topics

NAMD and VMD


Here are the web sites for NAMD and VMD, two of the early molecular modeling apps that make heavy use of GPU acceleration:

NAMD:  www.ks.uiuc.edu/Research/namd/

VMD:     www.ks.uiuc.edu/Research/vmd/

 

 


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Hex Protein Docking


The latest version 6.0 of Hex Protein Docking is available here with CUDA GPU support on Linux.

This version was released on 13 Jan 2010.

They also maintain a public server which is GPU enabled.


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LAMMPS


Certain LAMMPS pair-styles are GPU enabled. The Jan 15 2010 version includes:

Users should refer to the LAMMPS pages, including the section on running on GPUs.

Current documentation describes the speedup with each pair style.


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Latest Stories and Papers

Title New Replies Last postsort icon
New CUDA Toolkit Released New 0 new 01-26-2012
Accelerating the Near Non-bonded Force Computation in Desmond with Graphic Processing Units (IEEE) New 0 new 01-23-2012
Molecular Docking on FPGA and GPU Platforms (IEEE) New 0 new 12-15-2011
FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME (IEEE) New 0 new 12-14-2011
Exploring Fine-Grained Task-Based Execution on Multi-GPU Systems (IEEE) New 0 new 12-14-2011
Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator using GPUs (ACM) New 0 new 11-12-2011
Loose Capacity-Constrained Representatives for the Qualitative Visual Analysis in Molecular Dynamics (ACM) New 0 new 11-12-2011
High-performance Blob-based iterative reconstruction of electron tomography on multi-GPUs (ACM) New 0 new 11-12-2011
Preliminary Work on Graphics Processing unit Based Direct Simulation Monte Carlo (ACM) New 0 new 11-12-2011
FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME (ACM) New 0 new 11-12-2011
GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution: Real World Applications (ACM) New 0 new 11-07-2011
TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes (ACM) New 0 new 09-08-2011
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems (ACM) New 0 new 08-19-2011
Real-Time Rendering of Solvent-Accessible Surfaces for Molecular Models (ACM) New 0 new 08-16-2011
Immersive molecular visualization and interactive modeling with commodity hardware (ACM) New 0 new 08-06-2011
Molecular dynamics simulations on commodity GPUs with CUDA (ACM) New 0 new 08-06-2011

Latest Blog Posts

Title New Replies Last postsort icon
How to best achieve encapsulation on the GPU? New 1 new 09-11-2010

Latest Forum Posts

Title New Replies Last postsort icon
LAMMPS New 4 01-28-2012
NAMD and VMD New 7 11-11-2011
Hex Protein Docking New 1 10-19-2011
ACEMD New 0 02-09-2010
AMBER New 0 01-11-2010
HOOMD / HOOMD-Blue New 0 01-11-2010

Latest Events

Title New Replies Last postsort icon
High Performance Simulation of Biological systems at MAS 2012 New 0 new 01-02-2012
International Conference VipIMAGE 2011 - III ECCOMAS THEMATIC CONFERENCE ON COMPUTATIONAL VISION AND MEDICAL IMAGE PROCESSING New 0 new 03-16-2011
GPUs for Molecular Dynamics - GROMACS New 0 new 10-19-2010
Bio Workbench Seminar New 0 new 06-26-2010
Bio Workbench Seminar New 0 new 06-26-2010
Workshop on GPU Programming for Molecular Modeling New 0 new 06-22-2010
MoBS: Workshop on Modeling, Benchmarking, and Simulation New 0 new 05-03-2010
International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation New 0 new 05-03-2010
The 1st UK CUDA Developer Conference - Oxford, UK New 0 new 12-03-2009

Latest Code Snippets and Repositories

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Latest Wiki Pages

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