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.
  1. Launch NanoEngineer-1
  2. Choose Tools -> Preferences -> Plug-ins
  3. 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)
  4. 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)
  5. 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.