GROMACS 3.3.2 + HDF5 Patch #2
GROMACS (GMX) is an extremely high performance, open source, and cross-platform package used to perform molecular dynamics simulation of systems with hundreds to millions of particles. NE1 currently uses GROMACS+HDF5 as an energy minimization engine option. The +HDF5 comes from our experimental HDF5-based simulation results file format augmentation. The HDF5 file format won't affect non-HDF5 GMX operation. Also included with the binary installers is mcpp, a free, open source, portable C preprocessor. A C preprocessor is required for GROMACS use, so we've included one since some platforms don't come with one.
This is GROMACS 3.3.2 + HDF5 Patch #2 as of April 25, 2008.
Click the following links or visit the official GROMACS_HDF5 page to learn more about GROMACS+HDF5:
Installation Instructions
Windows
Run the GROMACS+HDF5 self-extracting installer "GROMACS_3.3.2+HDF5_p2.exe".
Mac OS X
Run the GROMACS+HDF5 self-extracting installer "GROMACS_3.3.2+HDF5_p2.dmg".
Linux and Developers
GROMACS+HDF5 must be compiled from sources for Linux users and developers. Download the GROMACS+HDF5 source distribution "GROMACS_3.3.2+HDF5_p2.tar.gz" and follow the instructions here: Building and Installing GROMACS+HDF5
Post-install Notes
If you have not installed this from the NanoEngineer-1 Suite installer you will have to modify your preferences to enable NanoEngineer-1 to use this plugin.
- Launch NanoEngineer-1
- Choose Tools -> Preferences -> Plug-ins
- Check the box for GROMACS and input the full path to the mdrun executable including its file name. For example, on Windows it may be C:\GROMACS_3.3.2+HDF5_p2\bin\mdrun.exe)
- Check the box for cpp and input the full path to the mcpp executable including its file name. For example, on Windows it may be C:\GROMACS_3.3.2+HDF5_p2\MCPP\bin\mcpp.exe)
- Click Ok.
Copyrights and Licensing
GROMACS is Free Software, available under the GNU General Public License.
Our modifications to the GROMACS code are Copyright 2007-2008 Nanorex, Inc. and fall under GROMACS's GPL license.
See source/HDF5_COPYING for HDF5 copyright and licensing details.
mcpp is open source software released under a BSD-style license. See MCPP/LICENSE for details.