SIMONAPreprocessor
Settings/Tools
D_Set_Main.png

Settings
  • Preprocessor settings
    • Preprocessor path: Put the path of the preprocessor here.
    • Verbose level: Higher integer means more output.
    • Enable expert mode: By checking this option, expert settings in all parts of the gui will be enabled.
    • Verbose dihedral output: If checked, more information about dihedrals within the simulated system will be created.
    • Never show XML tree: After creating the xml output, you will usually be asked if you want to display the file in SIMONAgui. If this option is checked, it won't be shown and you won't be asked.
  • PDB settings:
    • You can select which tool should be used for interacting with pdb-files.
    • If add CONECT entries is checked, in pdb output files will be CONECT entries.
    • Use the occ-column of pdb file as charge.
      D_Set_Set.png
Tools
  • PDB
    this Tool allowes you to extract a PDB file from an XML-file which was created by POEM++. To do so, enter path of input file and output file in the boxes and click Start.
    D_Set_Tools_PDB.png
  • This is an experimental function.
    D_Set_Tools_Gauss.png
GMC Molecules
  • Parameter-file: Enter the output path of the parameter file here.
  • Scan Mol2 file for parameters and add: The parameterfile will be created using the molecules added in the box. To add a molecule, select it and click Add molecule.
  • For every added residue the box will contain one entry containing information about it.
    In 'Structure' are lists of the Mol2AtomTypes, Charges, Bonds and Moves within the residue.
    In 'Forcefields' are lists of the forcefields and their parameteres. Some are preset, others have to be set. You may also change preset values due to your needs.
  • Save: When you have entered all information, click save. The parameter file can now be loaded by other GUI sections.
    D_GMC_Molecule.png