Molecular Dynamics in the Open
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README.md

README.md

What is OpenMD?

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 tag and must have two sections:

  1. a C-based section, and

  2. a block for initial coordinate and velocity information.

Detailed descriptions of the structures of these files are available in the "doc" directory. Sample simulations are available in the "samples" directory.

What you need to compile and use OpenMD:

  1. A good C++ compiler. We've built and tested OpenMD on the following architecture & compiler combinations:
Architecture CXX Notes
macOS 10.13.5 (intel) c++ (Apple LLVM version 9.1, Open MPI 3.0.0)
macOS 10.13.5 (intel) g++ (GNU version 6.4.0)
Linux (Ubuntu 18.04 - x86_64) g++ (GNU version 7.3.0, Open MPI 2.1.1)
Linux (RHEL 7.4 - x86_64) icpc (Intel version 18.0, Open MPI 3.0.0)

OpenMD uses features in the standard template library (STL). Most (but not all) C++ compilers support these features.

  1. CMake, a cross-platform build system which is available at http://www.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.

  2. 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: http://www.open-mpi.org/

  3. Other optional (but quite useful) libraries that will unlock some features of OpenMD:

  4. Some of the utility scripts depend on Python and Perl. These interpreters are common installations on most flavors of Unix and Mac OS X.

Instructions

  1. Get, build, and test the required pieces above.
  2. mkdir build
  3. cd build
  4. cmake ..
  5. make
  6. umask 0022; sudo make install

That's it.