CE-MolSim Training

Contents:

  • Timetable
  • Command-line primer
    • Connecting to a remote Linux computer
    • The command prompt
    • Getting familiar with basic commands
    • Exercises
    • Going further
  • Calculating properties of water with Gromacs
    • Background
    • Setting up your account on Balena
    • Scratch space
    • Preparing the simulation
    • Running the simulation
    • Visualising the dynamics with Vmd
    • Analysing the data
    • Investigating water properties
    • Questions
  • Calculating tnt solvation with Gromacs
    • Background
    • Drawing your tnt molecule
    • Converting tnt into the Gromacs format
    • Defining force-fields
    • Getting your topology file right
    • Checking your topology
    • Preparing the simulation box
    • Running the simulation
    • Exercises
  • Calculating Henry’s coefficients with Raspa
    • Background
    • Preparing the simulation
    • Running the simulation for Irmof-1
    • Running the simulation for UiO-66
    • Analysing the data
    • Going further
  • Analysing adsorption isotherms with MuSiC
    • Background
    • Preparing the analysis
    • Running a gcmc calculation in MuSiC
    • Getting raw isotherms
    • Converting fugacities to pressures
    • Understanding absolute and excess uptake
    • Producing snapshots
    • Tasks
    • Going further
  • Leveraging full nodes using Taskfarmer
    • Serial vs. parallel programs
    • Running serial programs on the cluster
    • Making the program available
    • Usage
    • Writing a task file
    • Submitting the job
  • How do you access Balena?
    • Logging in from the University computers
    • Logging from your Windows computer
    • Logging in from your MacOS or Linux computer
  • Accessing remote files
    • Accessing from university’s computers
    • Accessing files from Windows/MacOS
    • Accessing files from Linux
    • Accessing files from the command line
  • More about the command prompt
    • Useful conventions
    • Help, I am stuck!
    • Understanding what you type
    • What does command X do?
    • What’s the command to do Y?
    • What if something goes wrong?
    • How to edit a file?
    • How to look at file content?
  • How do you access specific programs?
    • Listing available modules
    • Loading modules
    • Unloading modules
  • How do you submit a job?
    • Writing a submission script
    • Submitting a job
    • Probing the state of your jobs
    • Getting the status of your calculation
    • Cancelling a job
CE-MolSim Training
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