Week 1¶
This week we will install most of the necessary software and familiarize ourselves with some basic concepts and background. In addition, getting used to the command line terminal is essential as it will be needed in almost everything.
Important
You must be able to install software on your computer.
You are responsible for running virus checks.
Always take a backup before any major installations.
Software installations include (done during labs and classes):¶
We will do this during the labs, please don’t do any installations beforehand.
First one of the following is needed:
For Mac users, Xcode is required. In addition, a package manager such as Homebrew or MacPorts. Most of the examples are with Homebrew.
For windows users: Windows subsystem for Linux WSL/ WSL2, virtual machine for Linux or dual boot Windows-Linux. We will discuss these options.
Linux users: nothing to do at this step.
For everyone to install:
We will do this during the labs, please don’t do any installations beforehand.
Python either using pip or Anaconda. The latter is used but the former is also ok.
Installing virtual environment is also highly recommended
Jupyter Notebook / Lab
C/C++ compilers and some other necessary software (needed for installing Gromacs later)
VMD (Visual Molecular Dynamics) for visualizing molecular data
Plain text (ASCII) editor
When will we install software?¶
The above installations will be done mostly during the first lab on Monday of Week 2 (=there is no lab on the first Monday).