OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. "sticky" atoms, point dipoles, and coarse-grained assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat interfaces, and nanoparticles) have all been simulated using force fields included with the code. OpenMD works on parallel computers using the Message Passing Interface (MPI), and comes with a number of analysis and utility programs that are easy to use and modify. An OpenMD simulation is specified using a very simple meta-data language that is easy to learn.
Simulations are started in OpenMD using a single Molecular Dynamics (.omd)
file. These files must start with the <OpenMD> tag and must have two
sections:
-
a C-based
<MetaData>section, and -
a
<Snapshot>block for initial coordinate and velocity information.
Detailed descriptions of the structures of these files are available
in the docs directory. Sample simulations are available in the
samples directory.
- A good C++17-compliant compiler. We've built and tested OpenMD on the following architecture & compiler combinations:
| Architecture | CXX | Notes |
|---|---|---|
| macOS Sonoma (intel & arm) | c++ | (Apple clang 15.3, Open MPI 5.0.2) |
| Linux (Ubuntu 23.10 - x86_64) | g++ | (GNU version 13.2 Open MPI 4.1.5) |
| Linux (RHEL 8.9 - x86_64) | icpc | (Intel version 19.1.3, Open MPI 4.0.1) |
OpenMD uses features in the C++ standard library and language features from C++17. Most (but not all) C++ compilers support these features.
-
CMake, a cross-platform build system which is available at cmake.org. Most Linux and some Unix distributions provide CMake as a standard package. If not, please download it, and make sure you get a recent version. Mac OS X users can either download the CMake installer or install it from the command line using macports.
-
An implementation of MPI-2 is optional for the single processor version of OpenMD, but is required if you want OpenMD to run in parallel. We like OpenMPI. Other implementations of MPI-2 might work, but we haven't tried. You can get Open MPI here: open-mpi.org
-
Other required libraries that unlock some features of OpenMD:
- Open Babel: openbabel.org
- Qhull: www.qhull.org
- FFTW: www.fftw.org
- Doxygen: www.doxygen.org
-
Some of the utility scripts depend on Python, NumPy, SciPy, and Perl.
These interpreters are common installations on most flavors of Unix and Mac OS X.
- Get, build, and test the required pieces above.
- mkdir build
- cd build
- cmake ..
- make
- umask 0022; sudo make install
That's it.