Lecture Notes

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Computational Chemistry (CCB 438/550), Spring, 2020

1. Course syllabus.

2. Getting an Amarel account: If you don't already have one, request a user account on Amarel by visiting https://oarc.rutgers.edu/access. Use a terminal application (or something like putty on Windows) to carry out a trial login.

3. Homework #1 Go through the following self-guided tutorials:
   
   • Basic Linux/Unix introduction
   • More in-depth coverage of the command line
   • Basics of AWK
   • (There is nothing to hand-in, but should be done by Jan. 31.)

4. Here is the XrayPrep script discussed in class on Jan. 27.

5. Here is the documentation for RDB; concentrate on the operators highlighted in yellow.

6. Homework #2, due Feb. 12 Assignment is here.

7. Homework #3, due Feb. 19 Assignment is here.

8. Homework #4, due Mar. 4 Assignment is here.

9. Notes on the COSMO solvation model.

10. Homework #5, now due Mar. 30 Assignment is here.

11. Remote Lecture 1: force fields.
    [Note: if you get spinning colored lines, click on pause, then again on play.] See also the slides in PDF format.

12. Remote Lecture 2: MD and TI. See also the slides in PDF format.

13. Homework #6, due Apr. 1 Assignment is here.

14. Project and Term Paper Instructions, (updated on 4/11).

15. Remote Lecture 3: Amber. See also the slides in PDF format.

16. Remote Lecture 4: MD. (There are no slides for this lecture.)

17. Homework #7, due Apr. 8 Assignment is here.

18. Remote Lecture 5: small molecules. See also the slides in PDF format.

19. Remote Lecture 6: free energies. See also the slides in PDF format.

20. Remote Lecture 7: more free energies. See also the slides in PDF format.

21. Homework #8, due Apr. 22 Assignment is here.

22. Remote Lecture 8: cycles and experiments. See also the slides in PDF format.

23. Remote Lecture 9: generalized Born models. See also the slides in PDF format.

24. Homework #9, no due date Assignment is here.

25. Remote Lecture 10: normal modes. See also the slides in PDF format.

26. Remote Lecture 11: normal modes plus QM/MM. See also the slides in PDF format.

27. Remote Lecture 12: more QM/MM. See also the slides in PDF format.

28. Remote Lecture 13: final thoughts. See also the slides in PDF format.
    
    (Click "next" to see lecture notes from previous semesters)