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These are the Materials For the Dartmouth Course CHEM101.6 "Computational Methods in Chemistry and Biophysics".   

We utilized the Zuckerman's "Statistical Physics of Biomolecules" as our primary textbook for this course. 

The course was structured with to have a 1.5 hour lecture and a 1.5 hour interactive jupyter notebook coding lab each week.

This repo contains jupyter notebooks for the 6 in class execrcises, and links to the recordings of 7 1.5 hour lectures.  

Each exercise had an in class demo portion, where I completed a portion of the notebooks interactively with the students, but I don't have video for many of these classes.

For some exercises, I have posted a second notebook that has the solutions to the classroom activities completed.  A few exercises have "Instructor Solutions" available as well.



Lecture 1 (Force Field & MD Basics) 

Lecture 1 Notes: 
https://www.dropbox.com/s/8strabjkktz78qc/CHEM101.6_W22_Lecture1_1.11.22.pdf?dl=0
https://www.dropbox.com/s/a92l53671ybouyt/CHEM101.6_W22_Lecture1_1.11.22.pptx?dl=0

Lecture 1 Video: 
https://www.dropbox.com/s/dyud7rw25s9i6so/CHEM101.6-W22_Lecture1_ForceFIelds_MDbasics.mp4?dl=0

Exercise 1:  (OpenMM Simulations of Butane, MD Traj Basics, Concepts From Zuckerman Chapters 1-2)
https://github.com/paulrobustelli/CHEM101.6/blob/main/Chem101.6_Project1_Classroom_Solutions_1.13.22.ipynb

Exercise 1 Solutions:
https://github.com/paulrobustelli/CHEM101.6/blob/main/Chem101.6_Project1_Classroom_Solutions_1.13.22.ipynb https://github.com/paulrobustelli/python_demos/blob/main/Chem101.6_Project1_Instructor_Solutions.ipynb

Lecture 2 (MD & Protein Structure Basics)

Lecture 2 Notes:
https://www.dropbox.com/s/tg7rjfhh12m85jv/CHEM101.6_W22_Lecture2_1.18.22.pdf?dl=0
https://www.dropbox.com/s/uchtd3cq72ie8hp/CHEM101.6_W22_Lecture2_1.18.22.pptx?dl=0

Lecture 2 Video:
part 1: https://www.dropbox.com/s/r7gsenuvieud8m1/CHEM101.6-W22_Lecture2_Part1_ProteinStructure.mp4?dl=0
part 2: https://www.dropbox.com/s/yp7wmafrrtiifah/CHEM101.6-W22_Lecture2_Part2_ProteinStructure.mp4?dl=0


Exercise 2 (VMD & Protein Dynamics Basics):
https://github.com/paulrobustelli/CHEM101.6/blob/main/CHEM101.6_Project2_Students.ipynb

Exercise 2 Class Portion: 
https://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=e018e7cd-110a-4735-9552-ae2301664532

Lecture 3 (Topics From Zuckerman Chapters 1-4) 

Lecture 3 Notes:
With Space for additional note taking:
https://www.dropbox.com/s/0lf0kaqgrc7p605/CHEM101.6_W22_Lecture3_1.25.22_blanks.pdf?dl=0
https://www.dropbox.com/s/hpnqc2eb4g0f5fi/CHEM101.6_W22_Lecture3_1.25.22_blanks.pptx?dl=0

Additional notes filled in:
https://www.dropbox.com/s/ph0ml80e3gasmjq/CHEM101.6_W22_Lecture3_1.25.22_notes.pdf?dl=0
https://www.dropbox.com/s/s62s5qqxnowuazb/CHEM101.6_W22_Lecture3_1.25.22_notes.pptx?dl=0

Lecture 3 Video:
https://www.dropbox.com/s/5ni4m8z7l409kgw/CHEM101.6-W22_Lecture3_Zuckerman_Ch1-4.mp4?dl=0

Exercise 3 (Ubiquitin Dynamics):
https://github.com/paulrobustelli/CHEM101.6/blob/main/CHEM101.6_Project3_UBQ_Students.ipynb

Exercise 3: Solutions:
https://github.com/paulrobustelli/python_demos/blob/main/CHEM101.6_Project3_Instructor.ipynb


Lecture 4 (Topics From Zuckerman Chapters 3-4, Protein Folding & Intrinsically Disordered Proteins)

Lecture 4 Notes: 
https://www.dropbox.com/s/wtf0jmovn8d5yhn/CHEM101.6_W22_Lecture4_2.1.22.pdf?dl=0
https://www.dropbox.com/s/45eb3qir98gw6st/CHEM101.6_W22_Lecture4_2.1.22.pptx?dl=0

Lecture 4 Video: 
https://www.dropbox.com/s/n3ptlg1b14nc43f/CHEM101.6-W22_Lecture4_ProteinFolding_IDPs.mp4?dl=0

Exercise 4 (Analyzing a Protein Folding MD Simulations)
https://github.com/paulrobustelli/CHEM101.6/blob/main/CHEM101.6_Project4_Student.ipynb

Lecture 5 (Protein Structure and Dynamics from NMR)

Lecture 5 Notes:
https://www.dropbox.com/s/so8lvb5pcn6vh78/CHEM101.6_W22_Lecture5_2.8.22.pdf?dl=0
https://www.dropbox.com/s/quj0z4yjl67vjk3/CHEM101.6_W22_Lecture5_2.8.22.pptx?dl=0

Lecture 5 Video:
https://www.dropbox.com/s/zh7s3ap5mayokd5/CHEM101.6-W22_Lecture5_NMR.mp4?dl=0

Lecture 6 (Enhanced Sampling - Replica Exchange & Metadynamics)

Lecture 6 Notes:
https://www.dropbox.com/s/m1gresone4xsdqo/CHEM101.6_W22_Lecture6_2.14.22.pdf?dl=0
https://www.dropbox.com/s/dtvn5jv1pb3qewx/CHEM101.6_W22_Lecture6_2.14.22.pptx?dl=0

Lecture 6 Video: 
https://www.dropbox.com/s/2s90mif1tvjchdk/CHEM101.6-W22_Lecture6_EnhancedSampling.mp4?dl=0

Exercise 5 (Alanine Dipeptide Metadynamics): 
https://github.com/paulrobustelli/CHEM101.6/blob/main/CHEM101.6_Project5_MetaDynamics_aladipeptide_student.ipynb
https://github.com/paulrobustelli/CHEM101.6/blob/main/Project5_MetaDynamics_aladipeptide_student.ipynb

Exercise 5 Class Solutions: 
https://github.com/paulrobustelli/CHEM101.6/blob/main/Project5_MetaDynamics_aladipeptide_class_solutions.ipynb 

Exercise 6 (Replica Exchange & Statistical Errors):
https://github.com/paulrobustelli/CHEM101.6/blob/main/Project6_repex_blockerrors.ipynb

Exercise 6 Demo (Replica Exchange & Statistical Errors From Blocking):
https://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=cb86ff15-2c80-47a5-9e77-ae4601678547

Lecture 7 (Water/Solvation & Ligand Binding) 

Lecture 7 Notes:
https://www.dropbox.com/s/9c6n1brakmfrzmv/CHEM101.6_W22_Lecture7_3.1.22.pdf?dl=0
https://www.dropbox.com/s/q2y3litmsg9d95a/CHEM101.6_W22_Lecture7_3.1.22.pptx?dl=0

Lecture 7 Video:
https://www.dropbox.com/s/83jih2xw3kgcxm1/CHEM101.6-W22_Lecture7_Water_LigandBinding.mp4?dl=0