CONFLEX Manual

Crystal structure optimization using cif file

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

CONFLEX/Sample_Files/CONFLEX/crystal/optimization/cif_file

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.cif" file.

    2. When opening a file, please select "Cif File (*.cif *.cmf)" as the file type.

    Crystal Opt 1

  2. Click the Label icon in the "Molecule Box" dialog box to check the serial number of the atom.

    3. In the step below, we will set the bond order of the double bond, so please check the atomic number here.

    Crystal Opt 2
  3. Select "CONFLEX" from the "Calculation" menu to display the CONFLEX Settings dialog.
    4. Crystal Opt 3
  4. Click "Detail Settings" in the CONFLEX Settings dialog to display the Detail Settings dialog.
    5. Crystal Opt 4
  5. First, set the type of calculation.

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

    Crystal Opt 5
  6. Next, set the optimization method.

    7. Select "ALL" from the "Crystal Optimization:" pull-down menu in the "Crystal Optimization" dialog on the lower left. The values in the cif file will be displayed for the lattice constants and space groups.

    Crystal Opt 6
  7. Click "Edit & Submit" in the Detail Settings dialog.
    8. Crystal Opt 7
  8. The bond order of the molecule is set by the "CIF_BOND=" keyword.

    9. Bonds between atoms 2-6 and 3-8 of the input molecule are double bonds, so change the 1 in "CIF_BOND=" to "2"

    CIF_BOND=(2,6,1)
    CIF_BOND=(3,8,1)
    ↓
    CIF_BOND=(2,6,2)
    CIF_BOND=(3,8,2)

    The serial number of the atoms are checked in the molecule window.

    Crystal Opt 8
  9. Make sure the bond orders are set correctly, and click "Submit".
    10. .

    The crystal structure optimization job will be started.

    Crystal Opt 9
  10. When the job is started, the "Job Manager" will be displayed.

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

    Crystal Opt 10-1

    Double-click to open the molecule window and view the optimized structure (tartronicacid-F.cif).

    Crystal Opt 10-2
    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 Opt 10-3
  11. The folder contains "tartronicacid.cif" and six other files:
    • tartronicacid.bsf
    • tartronicacid.bso
    • tartronicacid.ical
    • tartronicacid.ini
    • tartronicacid.sdf
    • tartronicacid-F.cif
    12. Crystal Opt 11