User’s guide

When you have installed Kvazar, you can start calculation by next command, typed in terminal:

kvazar config.cfg

Config.cfg file is file in Yaml format (.cfg or .yml). It should contains next lines:

  1. Mandatory lines:

    • calculation_mode : <option>

    There can be SINGLE_POINT or MOLECULAR_DYNAMIC (register is not important, you can write “molecular_dynamic”).

    • method : <option>

    There can be MARTINI, TB, REBO, AIREBO

    • input : path/to/file.ACD

    If configuration file and input file are in one directory, you should specify only name and extension of file: filename.extension (.ACD and .pdb are possible).

    • max_time : <value>

    Value of simulation time limit, if calculation mode is MOLECULAR_DYNAMIC.

    • output : filename.nmd

    The name and extension of output file. .nmd is the only one allowed extension for output file. It’s a zip-archive.

    • save_period : <value>

    It’s an integer value of period with which all parameters, velocities, coordinates will be saved.

  2. Optional lines:

    • thermostat : <option>

    There might be Nose-Hoover, Berendsen. Additionally, there might be “Dissipative”. It should be used if structure you are investigating is not optimized.

    • temperature : <value>

    There you should specify the temperature, that thermostat should maintain. In case of “Dissipative” thermostat, it is no need.

    • periodic_box : [[x1, y1, z1], [x2, y2, z2]]

    To use periodic boudnary conditions, you have to specify the sizes of periodic box - coordinates of two points, which define box unambigously.

    • cutoff_r : <value>

    There you can specify the value of cutoff radius.

    • dt : <value>

    dt is a time step in fs of simulation. Automatically it is equal to 1 fs. In case of chemical reactions (in AIREBO method) dt should be less or equal to 0.3 fs.

    • monitoring : [<option1>, <option2>, etc]

    There might be a list of options, that will be written on monitor and in files of parameters (f.e. “temperature” (it will be written in K), “energy” (in eV)) in output file and displayed in time of calculation.

    • maxwell_veloc : <option>

    There can be “yes” or “no”. You should specify the temperature for this option. Velocities are taken from Maxwell distribution according to specified temperature.

Example of configiration file can be found in /path/to/Kvazar/examples/

To start calculation of example file in directory /path/to/Kvazar/examples/water_box.ACD with MARTINI method type:

kvazar water_pbc_martini.cfg

There are a few more examples in /path/to/Kvazar/examples/ for other methods, as Tight-Binding, REBO and AIREBO.

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