Using Jamberoo

Use Jamberoo & Create Gaussian input

1. Molecular editors -->Jamberoo
2. Click Add fragment icon.
3. In 'Add Fragment' select Ring Fragments --> Cyclopentane
   
   Image I - Jamberoo 'Add Fragment' with Cyclopentane.
4. In Jamberoo main window click on the black background, then close the Add fragment window.
   
5. In 'Add Fragment' select Simple Fragments --> Nitro Group
                                                                                                                                                                                                                                                     Image II - Jamberoo 'Add Fragment' with Nitro Group.
6. In main Jamberoo window click on a H (cyan color)
7. Both molecules will be displayed linked together.
   
   Image III - Gaussian Input Creation
8. File → SEAGrid Export → Gaussian                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Image IV - Gaussian Input Export
9. Opens Gaussian 09 Input GUI. Say OK to the WARNING sign.
10. Methods → DFT → Common Hybrid Functionals → B3LYP. Select R - Restricted Closed - shell
11. Select - Basis Sets → Frequently-used basis sets → 6-31G. Say 'Yes' to Add Polarization d and/Or Diffuse Function.
    
12. In 6-31G options set, Sets of d functions on Heavy atoms and Sets of p functions on H atoms to 1.
    
13. Select 6-31+G in Diffuse functions.
    

14. Select Job-types → Commonly-used job Types → OptFreq

15. Select Keywords → Common Keywords → Pop. In Pop options select 'Minimal' and say done.

16. Select Keywords → Other Keywords and select GFInput, GFPrint and IOp options. In IOp options give Overlay - 6, options - 7, Value - 3. 

17. In Route section → choose use P

18. %nproc = 28 %mem (In MB) = 3000

19. Give checkpoint file a name: nitrocycp.chk

20. Job Title & Description: Nitrocycp RB3LYP/6-31+G(d,p) Pop=(Minimal) GFInput GFPrint Iop(6/7=3) Opt Freq

21. Charge =0 multiplicity = 1
    
    Image V - Gaussian Input Before Export
    

22. Done and export

23. Opens a create experiment window. In this change the experiment name (if you want to), Select the resource, queue and give 100 minute wall time.                                                                                            
    Image VI - Create Gaussian Experiment

24. Run it on bridges.psc.edu with RM queue.

View Gaussian Output in Jamberoo

1. Once the experiment is COMPLETED, from Expriment Summary page download the file to your local machine and open Jamberoo editor.
2. Navigate File → Open As → Gaussian → Gaussian G03 output
3. Select the file from your local machine.
4. Select the second option and OK.
   
   Image I - Select the output to visualize
5. Next window select OK.                                                                                                                                                                                                                                                                                                
   Image I - Selecting properties to show
6. In 'Vibration Control' select a frequnecy and select 'Animate Vibrations' in order to visualize the output.
   
   Image II - Selecting a vibration frequency to visualize the output