LAMMPS Installation

We suggest to install it from source files.

  • Download the latest stable version from https://lammps.sandia.gov/tars/lammps-stable.tar.gz

  • Extract tar file by tar xvf lammps-stable.tar.gz. This will create a folder named: lammps-29Oct20 (The date may change depending of the updates in the website). Rename lammps-29Oct20 folder to lammps.

  • Before keep going it is necessary to solve some dependencies: build-essential (to compile in C), MPIch (to work in parallel) , FFTW ( to compute long-range interactions), libxaw7 (to compute the movies). In one line code you choose

    sudo apt-get install build-essential libxaw7-dev

  • Then, go to the extract folder, and execute following commands. For provided example in FabMD, MOLECULE, KSPACE, and RIGID packages should be installed too.

    ~$ cd lammps
~/lammps$ cd src/STUBS
~/lammps/src/STUBS$ make clean
~/lammps/src/STUBS$ make
~/lammps/src/STUBS$ cd ..
~/lammps/src$ make clean-all
~/lammps/src$ make yes-molecule
~/lammps/src$ make yes-kspace
~/lammps/src$ make yes-rigid
~/lammps/src$ make serial

Note

If the installation part worked correctly, you should be able to find lmp_serial executable file inside lammps/src folder.

  • Modify machines_FabMD_user.yml to make the lammps_exec variable point to the location of the LAMMPS executable. e.g.

    ...
localhost:
        lammps_exec: "/home/hamid/lammps/src/lmp_serial"
    ...
...

NAMD Installation

We suggest to follow installation instructions from the NAMD website.

  • After installing NAMD, modify machines_FabMD_user.yml to make the namd_exec variable point to the location of the NAMD executable

    ...
localhost:
        namd_exec: "/home/hamid/opt/path/to/namd/sources/namd2"
    ...
...

GROMACS Installation

We suggest to use automate installer (source).

FabMD Installation

Before run LAMMPS test data set, you should install FabMD which provides functionality to extend FabSim3’s workflow and remote submission capabilities to LAMMPS specific tasks.