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://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6edd9f5a-7432-4964-b8d5-ae1a01642550 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://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=eb6b62f7-bb66-4163-9f45-ae210161da2d part 2: https://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b0302863-e828-4682-aea9-ae210162084f 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://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=57c45286-53fc-4388-9de8-ae28017044cc 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://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f5449522-05ee-4b71-916a-ae2f01659ffb 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://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d8a138fa-7e53-4b6e-9d28-ae3601686899 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://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0316c5e6-6121-4483-a114-ae3d0166404f 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) 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 Notes: https://dartmouth.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c8c0a806-81b2-4831-839c-ae4b016e0b72