SIMONAPreprocessor
Generic Monte Carlo - First Steps

How to do your first Generic Monte Carlo simulation.

This is just an example to get to know how this section works and what it does roughly. For more detailed information about all functions of POEM++ see here.

  • Startwindow
    Start the SIMONA Preprocessor by typing
    1 python simonagui.py
    into the shell (you have to be in the directory where simonagui.py is located). In opening window you can choose of which type your simulation should be. Now proceed to the Generic Monte Carlo section of the mainpage.

    3s_Mainpage.png

  • Input files
    In this step read in the *.mol2 file which you want to simulate. Therefore select Configuration at the menu on the left hand side. Type the path of the input-file in the box beside Input configuration. You may also browse the path by clicking the ... button beside the box. Also type the output-path in the box beside Output xml. To receive a file readable by SIMONA the file has to be *.xml. In the box 'Parameter file' has to be typed the path to a fitting parameter file. How to create such a file is described here.

    3s_Config_Input.png

  • Environment
    In this section the temperature has to be set. Temperature defines how free to move the molecules are. Either select Constant temperature or Geometric annealing. If constant temperature is selected only one temperature is to be entered in the box on the right. The temperature scale is in Kelvin. For a geometric annealed temperature Start temperature and End temperature are required. A standard simulation starts with a rather high, e.g. 500, while End temperature should be rather low, e.g. 5. But feel free to experiment with other settings.

    3s_Config_Envir.png

  • Simulation Settings
    For the outcome of a simulation the most important thing is the number of Simulation steps. The more you take, the better the result will be. But the needed calculation time will grow as well. Don't set more than 100.000 steps for your first try. Random seed should be selected.

    3s_Config_Settings.png

  • Forcefields
    In this section you have to choose which forcefields you want to use in your simulation. Select LennardJones in the drop down menu and click on Add forcefield to list.

    3s_Forcefields.png

    A popup will be shown. Select 3 as depth.

    3s_FF_Pop1.png

    In next popup select OpenCL

    3s_FF_Pop2.png

    In last popup set scale to 1.0 and press OK.

    3s_FF_Pop3.png


    Repeat this procedure for Coulomb electrostatics (all-atom). But instead of depth you will be asked for epsilon_r. Set it to 1.0.
  • Moves
    In this section you have to decide which moves the molecules in your simulation should perform. Select Rigid body translations and Rigid body rotations . Beside Rigid body translations set Delta[A] to 1.40 and beside Rigid body rotations set Delta[°] to 5.00. All other moves remain unchecked.

    3s_Moves.png

  • Output
    This section provides options for output settings. Select Std-, Trajectory- and Energy-output. Stepmod should be 1000. The Output filename of the trajectory has to have the ending *.pdb or *.vcf. A *.vcf file contains coordinates only, so is smaller, but can't be read by visualization tools. A *.pdb file contains additional information, so can be easily visualized.

    3s_Output.png

  • Generate XML
    Last step on the way to your *.xml is to let the Preprocessor do its work. On the top menu select Generate XML and wait until the output file has been created. The output file will be saved at the position you selected earlier. It is shown in the side menu section Preprocessor output.
  • Start SIMONA
    So far you have created an input file for SIMONA. To run SIMONA with your molecule and your settings. Type
    1 poempp <outputfile.xml>
    in the shell. <outpufile.xml> is here the outputfile you created with SIMONA Preprocessor. Make sure you are in the right directory. SIMONA will start its work and after some time creates the requested files.
  • Result
    To see the outcome use a visualization tool. In the trajectory file you can see the evolution of the process. The last step of the calculation is saved in *_snap.pdb.