Molecular Dynamics Lesson for Beginners with ChemCompute and MDAnalysis in a Jupyter Notebook
This lesson involves running a molecular dynamics simulation using ChemCompute then analyzing the simulation data in a Jupyter Notebook using the MDAnalysis library.
ChemCompute:
https://chemcompute.org/
Link to the Jupyter Notebook:
https://github.com/ggrazioli/ChemComp...
My website:
https://gianmarc.com/
How to install Anaconda:
• How to Install Anaconda - CHEM-101 at San ...
How to create a Jupyter notebook:
• How to make a Jupyter Notebook - CHEM-101 ...
0:00 – Introduction
0:07 – Overview: what we’ll do (ChemCompute + MDAnalysis)
0:38 – Installing libraries: MDAnalysis, NGLview, ipywidgets
1:39 – Why we import vs install in Jupyter
2:44 – Loading your molecule (1CSP example)
3:56 – Organizing project folders and file paths
4:54 – Loading the PDB into MDAnalysis
6:03 – Visualizing the structure with NGLview
7:27 – Measuring protein dimensions for the water box
8:05 – Using numpy arrays to find min/max coordinates
9:42 – Determining box size (≈80 Å) for solvation
12:16 – Setting up a simulation on ChemCompute
13:34 – Understanding simulation parameters and minimization
15:31 – Why simulations run remotely (clusters vs laptops)
17:19 – Submitting your job and what happens next
18:53 – Downloading results and organizing simulation files
20:53 – Loading simulation data (PSF + DCD files)
23:05 – Visualizing trajectories and adding water molecules
26:26 – Analyzing motion: RMSF (root-mean-square fluctuations)
28:05 – Selecting alpha carbons (CA) for backbone analysis
33:25 – Computing RMSF step-by-step in Python
40:57 – Plotting RMSF vs. residue ID
42:50 – Finding the most flexible residues with pandas
47:07 – Highlighting the “jiggly” residues in 3D
52:09 – Final visualization and wrap-up