IT notes

Useful IT notes and code snippets.

For new members of the group

• Pls, follow these instructions to connect to the IT infrastructure new_member.md

General

• Using conda environment manager - conda.md
• Using Jupyter Notebook/Lab/Hub - jupyter.md
• Configuring working Python environment using Sublime Text, Anaconda and Conda - subl_conda.md.
• Using git - git.md
• New Mac configuration - mac_conf.md

Molecular modeling

• Installing VMD, see vmd

Newton

• Rules
• Quick instructions
• Using SLURM (running tasks on cluster nodes)

Supercomputing

• Instructions on using Lomonosov/Lomonosov-2 supercomputer (in Russian) - here
• Quick instructions - here
• Running Gromacs on Lomonosov - here
• Running Gromacs with Plumed on Lomonosov - here
• Compiling Gromacs with Plumed on Lomonosov - here

Web technologies

• How to create web-site using GitHub pages and Jekyll gh-jekyll