Build a molecule

  1. Start Molden on Murska 
    2. >module load molden

>bsub -I molden
  2. Start Z-matrix editor (ZMAT Editor) from Molden Control

  3. Choose Add Line from the Zmatrix Editor and choose an atom from the perodic table. The first atom appears on Molden window

  4. To add the next atom: choose Add Line and then an atom and click on the first atom on the Molden window. Now you should see both atoms on the Zmatrix Editor as well as on the Molden window. Viewing mode can be changed from the Molden Control (Draw Mode).

  5. To add the third atom: click on an atom to which you want to bond a new atom. Then click on the remaining atom to define bond angle.

  6. For next atoms you need to define dihedral angles as well.

  7. Bond lenghts and angles can be edited on the Zmatrix Editor

  8. To rotate molecule: keep the left mouse button pressed and move the mouse.

Force field optimization

  1. Open a file containing molecular data or build a molecule from scratch

  2. Open ZMAT Editor and choose MapXYZ/Optimize. From drop down list choose Optimize with Tinker and klick OK.

  3. Set suitable settings for a job. Refer Tinker user guide for more details. Click GO when you are ready and then OK.

  4. Message will pop up when optimization is completed.

  5. Alternatively you can set up and launch optimization from Atom Attributes window. This window is opened by pressing the uppermost button (FF) in Molden Control window.

Submitting a Gaussian 03 job

  1. Open a file containing molecular data or build a molecule from scratch

  2. Open Zmatrix Editor

  3. Preoptimize with Tinker, if necessary.

  4. Choose the right Format: Gaussian and press Submit Job to open set up window.

  5. Methods etc. can be chosen from drop down lists and/or user can give own keywords. Extra options (%Mem, %NProcShered, ...) are added later. A job file can also be saved without submitting.

  6. Press Submit to proceed. This will open a xterm window, where you can add extra lines to your job file and finally submit you job.

  7. Two message windows appear. Click OK on both.

  8. Now give extra options for a Gaussian run. Follow the instructions.

  9. Finally, your job is submitted.

  10. To visualize your results: press Read from Molden Control and select a log file from the list.