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OpenMM Zephyr has been deprecated. We invite you instead to explore the OpenMM Script Builder web application, which provides a similar functionality. With pull-down menus and error checking, you can easily generate a script to run your simulation on OpenMM. Access the OpenMM Script Builder at http://builder.openmm.org. Read more about the OpenMM Script Builder and running scripts within OpenMM in Chapter 4 of the OpenMM Users' Guide at http://openmm.org. The current release of OpenMM Zephyr enables acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards and operating systems. To find out if your NVIDIA or ATI GPU is supported please see the Documentation Links section of the OpenMM Zephyr package. Need help? See the discussion forums (Advanced -> Public Forums) Citing: Please cite this website https://simtk.org/home/zephyr in any published work which utilizes OpenMM Zephyr
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0penMM Zephyr
Graphical user interface for running OpenMM version of Gromacs. To use Zephyr's visualization capabilities, you will also need to install VMD (optional but recommended).
Zephyr 2.0
Jul 08, 2010

Based on OpenMM 2.0. CUDA and OpenCL support provided. Explicit solvent simulations supported. NOTE: Due to ATI's implementation of OpenCL, GPU acceleration of explicit solvent simulations is only possible on their HD5000 series boards.Notes

Download Links

Windows

Sep 09, 2010
11 MB
Windows
Application/binary
OpenMM Zephyr 2.0 for Windows

Mac

Aug 02, 2010
22 MB
Mac OS X
Application/binary
OpenMM Zephyr 2.0 for Mac OS 10.5 or 10.6

Linux

Aug 02, 2010
17 MB
Linux
Application/binary
OpenMM Zephyr 2.0 for 32 bit Linux

Aug 02, 2010
21 MB
Linux
Application/binary
OpenMM Zephyr 2.0 for 64 bit Linux

VMD

Feb 12, 2010
0
Any
Application/binary
Link to molecular visualization program VMD. Required by Zephyr for visualizing simulation results.

Documentation Links

Zephyr User Guide

Sep 09, 2010
User guide to installing and running OpenMM Zephyr, with tutorial on running GROMACS-OpenMM from the command line

Find out if your GPU is supported

Feb 12, 2010
Follow this link to see if your NVIDIA GPU is supported

Sep 09, 2010
Follow this link to see if your ATI GPU is supported (explicit solvent acceleration only possible on HD5000 series boards)

Needed for supported GPU acceleration

Jul 08, 2010
Link to CUDA for NVIDIA GPUs. Need version 3.1 or later of the driver and toolkit (SDK code samples not required).

Jun 24, 2010
Link to OpenCL for ATI GPUs

Workshop Materials

Feb 12, 2010
Materials from OpenMM workshop June 24-26, 2009

Feb 12, 2010
Materials from RNA workshop June 19, 2009

PLEASE CITE THESE PAPERS

P. Eastman and V.S. Pande. "OpenMM: A Hardware-Independent Framework for Molecular Simulations." Computing in Science & Engineering, 12:34-39. (2010)

M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande. “Accelerating Molecular Dynamic Simulation on Graphics Processing Units.” J. Comp. Chem., 30(6), 864-872. (2009) View

Please cite: this code was made freely available on https://simtk.org/home/zephyr by the Simbios NIH National Center for Biomedical Computing. Simbios is supported by the National Institutes of Health through the NIH Roadmap for Medical Research Grant U54 GM072970 (2009)

ADDITIONAL PAPERS

P. Eastman and V.S. Pande. "Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations." J. Chem. Theor. Comput. 6:434-437. (2010)

P. Eastman and V.S. Pande. "Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit." J. Comput. Chem. 31:1268-72. (2010)


Additional GPL source code
Source code for Gromacs and FFTW binaries used in Zephyr, made available under GPL license.
Gromacs and FFTW for Zephyr 0.8
Jun 09, 2009

Download Links

Jun 09, 2009
0
Any
Source code
Link to FFTW download site. Required for building gromacs.

Jun 09, 2009
0
Any
Source code
Get source for Gromacs-OpenMM from OpenMM site for non-Windows builds of Gromacs-OpenMM

Jun 09, 2009
8 MB
Windows
Source code
Please do not use this for non-Windows builds. Gromacs source code modified to use OpenMM, CMake, and VMD.

Previous Releases


Gromacs and FFTW for Zephyr 0.2

Jan 27, 2009

Download Links

Jan 27, 2009
3 MB
Any
Source code
FFT library from http://www.fftw.org/

Jan 26, 2009
9 MB
Any
Source code
Gromacs source code modified to use OpenMM, CMake, and VMD


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