CE-Molsim documentation

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