Welcome to Pablito’s playground

Cheat codes

• Useful commands
  • Bash and general commands
  • Set up new computer cluster
  • Git set up
  • Git commands
  • Vim commands
  • Create hotspot on linux mint
• Things to do after installing Linux Mint
  • During the installation
  • Setting up Linux Mint
  • Copy important files and folders
  • Add SSH key to git
  • Package installations
• Install printers
• Compile CPMD
  • Cloning CPMD
  • On the LCBC cluster at EPFL
  • On my laptop
• Formating strings in Python
  • Basic formatting
  • Table summary
  • Useful examples
• Add and run CPMD regtests
• LSDalton memo
• GIMP
  • Autocrop all layers

Tutorials

• Equilibration at MM and QMMM level using Amber and CPMD
  • Generate RESP charges with Gaussian
  • Generate .mol2 file for leap and Amber
  • Leap (Amber): solvate molecule in TIP3P water
  • Generate custom box with packmol
  • Leap (Amber): set up a non-standard system from a .pdb file
  • Leap (Amber): custom solvent box
  • Amber: equilibrate system
  • Run QM/MM calculations with CPMD
• Visualize canonical orbitals from CPMD
  • Step 1: Get the CPMD files for the orbitals to plot
  • Step 2: Generate cube files

Links

• Documentation of the comp_chem_py library: https://comp-chem-py.readthedocs.io
• Introduction to Coupled Cluster Theory: https://cc-lecture.readthedocs.io
• VMD Quick help page (very useful when writing vmd scripts): http://www.ks.uiuc.edu/Research/vmd/vmd_help.html

Publications

A complete list of my scientific publications can be found on:

• My google-scholar account: https://scholar.google.com/citations?user=ZKpbiOUAAAAJ
• My ORCID account: https://orcid.org/0000-0001-7233-645X
• My PhD thesis: “Coupled Cluster theory for large molecules”.

Stuff not work related (in french)

• Le complot de la connaissance
  • Mon univers de la connaissance

Contact

• Pablo Baudin
• Scientific collaborator at LCBC, EPFL: https://lcbc.epfl.ch
• email: pablo.baudin@epfl.ch