#Basics
#Setting up your computer to have a terminal:
Mac: You have one! Search for “terminal” in your apps.
Linux: You have one! Search for “terminal” in your apps.
Windows: https://ubuntu.com/tutorials/ubuntu-on-windows#1-overview
Alternative: VSCode is bundled with a terminal
https://code.visualstudio.com/download
#Setting up your computer to connect to the supercomputer:
Using commands in the terminal and on the supercomputer:
bash: https://towardsdatascience.com/basics-of-bash-for-beginners-92e53a4c117a
slurm (supercomputer only): https://stanford-rc.github.io/docs-earth/docs/slurm-basics
vim: https://danielmiessler.com/study/vim/
emacs: https://www.gnu.org/software/emacs/tour/
Connecting to the supercomputer:
ssh: https://www.hostinger.com/tutorials/ssh/basic-ssh-commands
ssh-keygen: https://www.ssh.com/academy/ssh/keygen
Uploading/downloading files:
scp: https://linuxize.com/post/how-to-use-scp-command-to-securely-transfer-files/
#Setting up your computer as a workspace:
conda: https://conda.io/projects/conda/en/latest/user-guide/getting-started.html
ambertools: https://anaconda.org/conda-forge/ambertools
github: https://guides.github.com/activities/hello-world/
#Visualizing molecules:
chimera: https://www.cgl.ucsf.edu/chimera/download.html
chimerax: https://www.cgl.ucsf.edu/chimerax/download.html
vmd: https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
molview: https://molview.org/
#Computational Chemistry: Code practices, software development, and education:
MolSSI: http://education.molssi.org/
Beginner python: https://py.checkio.org/
https://www.learnpython.org/
Scientific python: https://stanford.edu/~schmit/cme193/lectures.html
numpy: https://cs231n.github.io/python-numpy-tutorial/
Quantum chemistry: http://vergil.chemistry.gatech.edu/notes/
#Classical molecular dynamics:
Amber MD: https://ambermd.org/tutorials/
OpenMM: http://docs.openmm.org/latest/userguide/library/03_tutorials.html
cpptraj/pytraj analysis: https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml#magicparlabel-3113 https://amberhub.chpc.utah.edu/cpptraj-cookbook/
#Machine learning
pandas: https://github.com/jvns/pandas-cookbook (Has online version to test without installing) https://www.activestate.com/blog/how-to-clean-machine-learning-datasets-using-pandas/
pytorch: https://pytorch.org/tutorials/
keras: https://www.tensorflow.org/tutorials https://keras.io/guides/
#Graphing and utilities
Plot digitizer: https://automeris.io/WebPlotDigitizer/
matplotlib: https://matplotlib.org/
Jupyter notebook: https://jupyter.org/
Classes⌗
Fall: Structure and Function of Biomolecules (5600/7600)
Winter: Computational Chemistry (6440/7440)