Bio-molecular modeling 2022

Welcome to Biomolecular modeling 2022.

Hello world!

What is this?

This repo contains install.sh, a script for installing course software on under Ubuntu.

Do I need ubuntu for the course?

Yes, you do, but do not worry, we will show how to get it and also remove it when the course is over (if you are not already runing linux, that is).

Not a linux user already?

If you are using MacOS or Windows, we will simply install VirtaulBox and run Ubuntu on your existing opertaing system.

1. Download the Ubuntu 20.04.4 iso image
2. Download and install virtualbox

   • Open VirtualBox and select New and give the VM a Name such as Ubuntu.

   • Allocate at least 1024 MB of memeory to the VM.

   • Create a virtual hard disk and make it a minimum 50GB in size and Dynamically allocated.

     • If you plan on keeping the VM after the course, we recommend going for 100 GB fixed size.

   • When starting the VM for the first time you wil be asked to select a virtual optical disk file. This is where you point to the recently downloaded Ubuntu iso file.

   • Install ubuntu by selecting the downloaded ubuntu iso file as your Media source.

   • Finish the installation as minimal install.

NOTE: If you have the new M1 macbook, virtual box will not work. Use - https://www.parallels.com/eu/

How to install course software (Ubuntu / VM)

Open a command line and install git:

sudo apt-get install git

When git is installed, clone this repo:

git clone https://github.com/isaksengeir/biomolmod

Move into biomolmod and run the install script

cd biomolmod
./install.sh

This will thake ~30 minutes depending on your internet connection. When the install script is done, restart the terminal window, and you should be all set for some molecular modeling.

TigerVNC

VNC server: desktop.saga.sigma2.no:5901

MacOS

Install Homebrew

copy paste this command into your terminal

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install TigerVNC with brew

brew install tiger-vnc

Homebrew puts the vncviewer executable here /usr/local/Cellar/tiger-vnc/1.12.0/bin/, but normally it can be launched by typing vncviewer in the terminal.

Windows

Go to https://tigervnc.org and follow instrucions to get a suitable self contained binary for your system.

Time schedule

Mon April 4th

• 09:15 - 12:00
  • Coffee, meet & greet (BOB/GVI)
  • Software install etc (GVI)
  • Basic Bash & SSH (GVI)
  • VR lab session (DS)
• 13:15 - 14:00:
  • Lecture: Basics force fields (BOB)
• 14:15 - 15:00:
  • Becoming a command line ninja: basic Bash, ssh and scp.

Tue April 5th

• 09:15 - 10:00:
  • Lecture: Simulations (BOB)
• 10:15 - 11:00:
  • Lecture: Free energy perturbation (Bob)
• 11:15 - 13:00:
  • Practical: Ion hydration in water (Bob)
• 13:00 - 15:00:
  • Lecture: DFT (GVI)
  • Gaussian / GaussView / Molden chemREACT
  • Practical: DFT reference reaction

Wed April 6th

• 09:15 - 10:00

  • DFT practical

• 10:15 - 12:00

  • Lecture: Empirical Valence Bond (GVI)
  • Qgui

• 13:00 - 15:00:

  • DFT practical
  • EVB practical

Thu April 7th

• 09:15 - 10:00
  • Practicals
• 10:15 - 11:00
  • Repetition (BOB)
• 11:00 - 15:00
  • Practicals

Fri April 8th

• 09:15 - 10:00
  • Practials / report
• 10:15 - 11:00
  • Popular science talk by Johan Åqvist
• 11:15 - 12:00
  • ENDEX