CONFLEX Manual

Crystal Structure Search

In this section, we will use the "tartronicacid.mol" file in the following folder as an example: 

CONFLEX/Sample_Files/CONFLEX/crystal/search

Please copy this file to an appropriate location under your home directory and work on it.

  1. Click "Open" from the "File" menu to open the copied "tartronicacid.mol" file.
    2. Crystal Search 1
  2. Select "CONFLEX" from the "Calculation" menu to display the CONFLEX Settings dialog.
    3. Crystal Search 2
  3. Click "Detail Settings" in the CONFLEX Settings dialog to display the Detail Settings dialog.
    4. Crystal Search 3
  4. First, set the type of calculation.

    5. Select "Crystal Search" from the "Calculation Type:" pull-down menu in the "General Settings" dialog on the top left.

    Crystal Search 4
  5. Next, set the optimization method.

    6. Select "Rigid" from the "Crystal Optimization:" pull-down menu in the "Crystal Optimization" dialog on the lower left.

    Crystal Search 5
  6. Next, set the search method in the "Crystal Search" dialog at the bottom right.

    7. Set each of the following:

    Rotation Method:
    Grid
    Rotation Step:
    30.00
    Position Prediction Method:
    Random
    Trial Structures:
    20
    Crystal Search 6-1

    Set the space group of the search to "P212121".

    Click "Select" button on the right of "Search Space Group:" and check "P212121" in the dialog that appears.

    Make sure all other checkboxes are unchecked and click "OK".

    Each setting will affect the search results. For details on each setting, please refer to the manual or tutorial for details on each setting.

    Crystal Search 6-2
  7. Click "Submit" button in the Detail settings dialog.

    8. The crystal structure search job will be started.

    Crystal Search 7
  8. When the job is started, the "Job Manager" will be displayed.

    9. After confirming that the "State" is "Finished", double-click on the row indicated by the red frame.

    Crystal Search 8-1

    The crystal structure obtained from the search is displayed in the molecule window that opens by double-clicking. Other crystal structures are listed in the "Property Box" dialog, and by clicking on an energy value, its crystal structure will be displayed in the molecule window.

    To view the packing structure, click on the "Controller" icon in the Molecule Box dialog
    , and then click on the "Packing" button in the toolbar that appears in the Molecule window.
    Crystal Search 8-2
  9. The folder contains "tartronicacid.mol" and seven other files:
    • tartronicacid.bso
    • tartronicacid.cpt
    • tartronicacid.csp
    • tartronicacid.ical
    • tartronicacid.ini
    • tartronicacid-FCS.cif
    • tartronicacid-PCS.cif
    10. Crystal Search 9