1. See also note.md file for detail.
  1. Compilation:
    REIN main program
    For MPI-1
    $ cd src
    $ ./configure.sh x86_64 ifort nospawn

    For MPI-2
    $ ./configure.sh x86_64 ifort

    For K computer
    $ ./configure.sh sparc k

    Then,
    $ make; make install

    Supporting software
    $ cd tools
    $ ./configure.sh x86_64 gfortran
    $ make; make install

    Execution:
    Copy all executable files and template directory.
    $ cd example/remd/namd
    $ cp -r ../../bin/* .
    $ input_builder ib.inp
    $ batch_builder bb.inp
    $ qsub rein.sh

    For K computer
    $ pjsub rein.sh

    Restarting the rein.
    $ batch_builder bb.inp restart
    $ qsub rein.sh

    Post simulation:
    Modify the rc.inp and run remd_converter
    $ ./remd_converter rc.inp