CUDA-accelerated Molecular Modeling Applications

CUDA-accelerated ion placement for STMV virus structure

Modern graphics processing units (GPUs) contain hundreds of arithmetic units and can be harnessed to provide tremendous acceleration for many numerically intensive scientific applications. The key to effective utilization of GPUs for scientific computing is the design and implementation of efficient data-parallel algorithms that can scale to hundreds of tightly coupled processing units. The use of several GPUs at a coarser level of parallelism can bring even more computational power to bear on highly parallelizable computational problems. NVIDIA CUDA enables GPUs programming in a variation of the C programming language. A working CUDA installation is required to run the software provided on this page.

Research Publications and Additional Information

• GPU accelerated molecular modeling research page

CUDA-accelerated test versions of VMD and example data

CUDA 1.1

VMD 1.8.7a19 CUDA binaries and test data (3/20/2008)
• VMD 1.8.7a19, for CUDA 1.1 (32-bit Linux)
• VMD 1.8.7a19, for CUDA 1.1 (64-bit Linux)
• VMD 1.8.7a20, for CUDA 1.1 (MacOS X Intel 10.5.2), (will not run on older versions of MacOS X, nor on PowerPC)
• VMD time-averaged Coulomb potential test data

CUDA-accelerated test versions of VMD, NAMD, cionize, and example data

CUDA 1.0

VMD 1.8.7a4 CUDA binaries and test data
• VMD 1.8.7a4, for CUDA 1.0 (32-bit Linux)
• VMD 1.8.7a4, for CUDA 1.0 (64-bit Linux)
• VMD time-averaged Coulomb potential test data

Cionize CUDA binaries and test data
• cionize, for CUDA 1.0 (32-bit Linux)

NAMD CUDA binaries and test data (not for production runs)
• NAMD/VMD, CUDA 1.0, interactive molecular dynamics demo (includes 32-bit and 64-bit NAMD binaries)

Intel C/C++ 9.0 CPU builds (for comparison, do not use for production runs)

• VMD 1.8.7a3, Intel C/C++ 9.0 (32-bit Linux)

GNU GCC CPU builds (for comparison)

• VMD 1.8.7a3, GNU GCC (32-bit Linux)
• VMD 1.8.7a3, GNU GCC (64-bit Linux)

Related software

• VMD -- Molecular visualization and analysis
• NAMD -- Molecular dynamics simulation
• NVIDIA -- Makers of the Tesla, Quadro, and GeForce devices used by GPU-accelerated apps listed above

Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at UIUC
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