SimTK: OpenMM Zephyr: Downloads

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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

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 View License

Download Package

Download Links

Windows

InstallZephyr-2.0.3-win32.exe

Sep 09, 2010

11 MB

Windows

Application/binary

OpenMM Zephyr 2.0 for Windows

Mac

Zephyr2.0.3.dmg

Aug 02, 2010

22 MB

Mac OS X

Application/binary

OpenMM Zephyr 2.0 for Mac OS 10.5 or 10.6

Linux

InstallZephyr-2.0.3-Linux32.sh

Aug 02, 2010

17 MB

Linux

Application/binary

OpenMM Zephyr 2.0 for 32 bit Linux

InstallZephyr-2.0.3-Linux64.sh

Aug 02, 2010

21 MB

Linux

Application/binary

OpenMM Zephyr 2.0 for 64 bit Linux

VMD

VMD (URL)

Feb 12, 2010

Any

Application/binary

Link to molecular visualization program VMD. Required by Zephyr for visualizing simulation results.

Documentation Links

Zephyr User Guide

ZephyrUserManual.pdf

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

NVIDIA supported GPUs (URL)

Feb 12, 2010

Follow this link to see if your NVIDIA GPU is supported

ATI Supported GPUs (URL)

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

CUDA, OpenCL for NVIDIA GPUs (URL)

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).

OpenCL for ATI GPUs (URL)

Jun 24, 2010

Link to OpenCL for ATI GPUs

Workshop Materials

OpenMM workshop June 2009 (URL)

Feb 12, 2010

Materials from OpenMM workshop June 24-26, 2009

RNA Workshop June 2009 (URL)

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 Package

Download Links

FFTW (URL)

Jun 09, 2009

Any

Source code

Link to FFTW download site. Required for building gromacs.

OpenMM download page (URL)

Jun 09, 2009

Any

Source code

Get source for Gromacs-OpenMM from OpenMM site for non-Windows builds of Gromacs-OpenMM

Gromacs-4.0.5-for-OpenMMZephyr-0.8-Source.tar.gz

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 Package

Download Links

fftw-3.2.tar.gz

Jan 27, 2009

3 MB

Any

Source code

FFT library from http://www.fftw.org/

Gromacs4.3pre_for_OpenMMZephyr0.2_Source.tar.gz

Jan 26, 2009

9 MB

Any

Source code

Gromacs source code modified to use OpenMM, CMake, and VMD

SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.

Version 4.2.2. Website design by Viewfarm. Icons created by SimTK team using art by GraphBerry from www.flaticon.com under a CC BY 3.0 license. Forked from FusionForge 6.0.5.

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