Cookbook

Home

• Basics (start here)
  • .bashrc Files
  • Run Jupyter Notebooks on a Compute Node
  • Use git
  • Install JAX
  • How to write a paper
  • How to make bibliographies
• Python
  • Figure Creation
  • Introductory Jupyter Modules
• Midway Essentials
  • Notes on Midway Modules
  • Running Jobs on Midway
  • Ensemble Jobs on Midway
• Molecular Dynamics Essentials
  • GROMACS 2019.4 with GPU Support
    • Run GROMACS on the GM4 Cluster
  • Building a System with CHARMM-GUI
  • MDP Options
  • Energy Minimization and Equilibration
  • PLUMED Tips and Tricks
  • VMD Rendering Guide
  • VMD as an Analysis Tool
• MD Intermediate Skills
  • Installing GROMACS
  • Replica Exchange Umbrella Sampling (REUS.md)
  • Alpha-Helical Content of Proteins
  • Markov State Modeling
  • Dynamical Galerkin Approximation
• AFINES
  • Installing AFINES
  • AFINES Branches
• Troubleshooting Articles
  • [GM4] Only one job runs at a time
  • [MD/VMD] "Expected integer but got 08" Error When Running TCL Script
  • [Midway] Modules need to be repeatedly loaded/unloaded before they work on a compute node
  • [Midway] I accidentally deleted a file!
  • [Midway] Help! I've lost write permissions!
  • [MD] Mpiexec error prevents simulations from running
  • Matplotlib animations don't work on Midway
  • Parallel jobs only taking up one node of a multi-node job
  • ThinLinc stops working after installing Anaconda
  • [Midway] Intel MPI isn't working
  • I can't run multiple Jupyter notebooks with GPUs in Jax
  • I can't use github commands on midway, authentication failed
  • Can't install GPU packages from conda-forge