OpenMD

Molecular Dynamics in the Open

Archive for January, 2010

OpenMD version 1.0.1

Jan 29

Posted by Dan Gezelter in News | No Comments

We are pleased to announce the release of OpenMD version 1.0.1 This version is largely a bugfix release, and is recommended for all users of OpenMD.  New things include:

  • Fixed the install procedures in the samples  and forceField directories.
  • Fixed Restraints, RestReader and RestWriter so that they work in parallel simulations.
  • Added a few new keywords to control how the constant-pressure hull method is invoked.
  • Added include lines for compatibility with gcc 4.4

Building and Installing OpenMD 1.0

Jan 29

Posted by Dan Gezelter in Examples | 5 Comments

NOTE: As of OpenMD version 2.0, the build system has changed significantly. We have an updated set of instructions to build and install OpenMD 2.0.

We’re going to assume here that you have already built and installed all of the prerequisites. If you haven’t done that, go install all of the required stuff and come back. We’ll wait.

OK, now that you’ve got all the stuff you need, we’ll branch to the same three architectures and give the instructions separately:

On a Mac (OS X 10.5 or greater)

  1. Download the latest release of the OpenMD:
    curl -o openmd-1.1.5.tar.gz http://openmd.org/releases/openmd-1.1.5.tar.gz
  2. Unpack the file:
    tar -zxvf openmd-1.1.5.tar.gz
  3. Change into the OpenMD directory:
    cd openmd-1.1.5
  4. Set the compiler variables to your preferred compilers:
    export CC=/opt/local/bin/openmpicc
    export CXX=/opt/local/bin/openmpic++
    export FC=/opt/local/bin/openmpif90
    export MPICC=$CC
    export MPICXX=$CXX
    export MPIFC=$FC

    All of the previous lines assume you are using /bin/sh or /bin/bash as your shell. If you are a csh/tcsh person, those environment variable lines will look like this:

    setenv CC /opt/local/bin/openmpicc
    setenv CXX /opt/local/bin/openmpic++
    setenv FC /opt/local/bin/openmpif90
    setenv MPICC $CC
    setenv MPICXX $CXX
    setenv MPIFC $FC
  5. Run the configure script with all of the arguments set to point to the correct locations for the optional software:
    ./configure --with-openbabel=/opt/local --with-qhull=/opt/local \
    --with-fftw=/opt/local --prefix=/opt/local
  6. Make OpenMD:
    make

    (This would be a good time to grab coffee. Perhaps lunch. Or maybe a quick trip to the pub would be in order.)

  7. Install OpenMD:
    sudo make install
  8. That’s it! When these steps are complete, OpenMD has been installed in the directory /opt/local/openmd. All of the programs are installed in the bin subdirectory, and samples are in the samples subdirectory, and required data files are in the forceFields directory.

On Linux

  1. Download the latest release of the OpenMD:
    curl -o openmd-1.1.5.tar.gz http://openmd.org/releases/openmd-1.1.5.tar.gz
  2. Unpack the file:
    tar -zxvf openmd-1.1.5.tar.gz
  3. Change into the OpenMD directory:
    cd openmd-1.1.5
  4. Set the compiler variables to your preferred compilers:
    export CC=/usr/bin/openmpicc
    export CXX=/usr/bin/openmpic++
    export FC=/usr/bin/openmpif90
    export MPICC=$CC
    export MPICXX=$CXX
    export MPIFC=$FC

    All of the previous lines assume you are using /bin/sh or /bin/bash as your shell. If you are a csh/tcsh person, those environment variable lines will look like this:

    setenv CC /usr/bin/openmpicc
    setenv CXX /usr/bin/openmpic++
    setenv FC /usr/bin/openmpif90
    setenv MPICC $CC
    setenv MPICXX $CXX
    setenv MPIFC $FC
  5. Run the configure script with all of the arguments set to point to the correct locations for the optional software:
    ./configure --with-openbabel=/usr --with-qhull=/usr \
    --with-fftw=/usr --prefix=/opt/local
  6. Make OpenMD:
    make

    (This would be a good time to grab coffee. Perhaps lunch. Or maybe a quick trip to the pub would be in order.)

  7. Install OpenMD:
    sudo make install
  8. That’s it! When these steps are complete, OpenMD has been installed in the directory /opt/local/openmd. All of the programs are installed in the bin subdirectory, and samples are in the samples subdirectory, and required data files are in the forceFields directory.

On Windows

You’re largely on your own here, because we don’t have a windows machine on which to test OpenMD, but if you have cygwin installed, it should be quite similar build instructions to Linux.

OpenMD version 1.0

Jan 14

Posted by Dan Gezelter in News | 1 Comment

We are pleased to announce the release of OpenMD version 1.0. This version is a substantial rewrite and includes many new features relative to our old code (OOPSE):

  • A new MD (meta-data) input file format
  • Amber force field and numerous other changes to aid in protein simulation
  • New Hydrodynamics code to allow Langevin simulation of rigid bodies of arbitrary shapes (this is particularly useful for coarse-grained simulations)
  • New electrostatics code including the efficient damped-shifted-force method
  • A new Langevin Hull constant pressure algorithm

Installing OpenMD prerequisites

Jan 13

Posted by Dan Gezelter in Examples | 7 Comments

To get OpenMD up and running, there are some required (and optional) software packages you should have to create a functioning build environment:

On a Mac (macOS Mojave or later)

  1. Install Xcode
  2. Install homebrew
  3. Open a Terminal window, and update your homebrew packages to the latest updates: 
    brew update
    brew upgrade

    (Note that the brew command is usually located in /usr/local/bin)

  4. Install the relevant prerequisite packages: 
    brew install cmake open-babel qhull zlib fftw open-mpi numpy scipy

    You can go have lunch or coffee while these are being built and installed.

  5. Install some optional software if you want to use and interact with the data produced by OpenMD: 
    brew install grace brewsci/bio/jmol
  6. Install some optional software if you want to develop or add to OpenMD: 
    brew install antlr@2 gengetopt doxygen

On Linux

  1. Use yum, apt-get, or the package manager in your favorite distribution to install the following packages and all of their prerequisites. Package names depend on the Linux variant, so in Fedora (and Red Hat) the package names are: 
    fftw
fftw-devel
cmake
    openbabel
openbabel-devel
openmpi3
openmpi3-devel
    python3-numpy
    python3-scipy
qhull
qhull-devel
zlib
zlib-devel

    In Ubuntu (and probably other Debian-based versions), the packages are:

    libfftw3-3
libfftw3-dev
cmake
openbabel
libopenbabel-dev
openmpi-bin
libopenmpi-dev
    python3-numpy
    python3-scipy
qhull-bin
libqhull-dev
minizip
zlib1g-dev
  2. Install some optional packages if you want to use and interact with the data produced by OpenMD: 
    jmol
grace
  3. Install some optional software if you want to develop or add to OpenMD: 
    antlr
    gengetopt
    doxygen

On Windows

Building and installing OpenMD on Windows is now quite straightforward. All it takes is the installation of an Ubuntu subsystem on your Windows Machine. Once you have this, all the commands for the Linux build are exactly the same. Alternatively, CMake will generate a (mostly) working build of OpenMD 2.6 in Windows with the Visual Studio 2019 C++ compiler, but we don’t routinely test the code in this configuration. 

  1. Follow the steps to building and installing OpenMD on Windows. (Note that if you’re planning on using visualization software that relies on an X Server, you’ll need to follow the Windows-specific instructions for that as well.)
  2. Refer to the list of packages for linux above to get the correct packages installed.

Building from source

If you are building all of the prerequisites from source, you’ll need (in addition to a C++ compiler):

  1. CMake – This cross-platform build system is required for building OpenMD.  You need to install CMake 2.8.11 or newer. This is available as a binary package from the KitWare website; alternatively, it may be available through your package manager (on Linux). If necessary, you can also compile it yourself from the source code.
  2. python – An interpreted scripting language that some of the OpenMD utilities use to parse and process data files.
    You probably already have this.
  3. Open MPI – A very good implementation of the MPI-2 specification for parallel computing.
  4. qhull – A computational geometry toolbox for computing convex hulls and Delaunay triangulations. qhull is required for the LangevinHull integrator and for any of the tools that compute the Hull atoms or hull volumes of nanoparticles and clusters.
  5. openbabel – a chemical toolbox for converting between different data formats.  This is required for building the atom2omd program which helps prepare initial “metadata” or omd files for simulations.
  6. fftw – a library for computing discrete Fourier transforms. This is required for surface undulation spectra (Hxy in staticProps). Get version 3.
  7. zlib – required to support reading compressed trajectory files.

You’ll also likely want to download and compile the following useful tools for interacting with the data:

  1. Jmol
  2. xmgr
  3. grace
  4. NumPy
  5. SciPy
  6. vmd

If you are going to be extending or developing OpenMD, you’ll need the following tool:

  1. antlr – our tool for parsing meta-data files.  You’ll want version 2.7, not 3.
  2. gengetopt – a tool to generate C code to parse the command line arguments argc and argv that are part of every C or C++ program

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