Lessons Assignment 1

Assignment 1 - Linux Intro and Turbomole Test Calculations

Made for use in ME 4331.

Task 1 - Make your account public

• Listen to the commands Jeremy will give during the meeting and run them.

bash /home/jerschro/Scripts/chmod/fix_chmod.sh

* This is a bandaid to the issue of not everyone being in the same group but it works.

Task 2 - Add Turbomole .bashrc information.

• Copy the text below to your .bashrc file. You may also want to add the aliases listed here. When added, run the command source .bashrc.

export TURBODIR=/home/aaquino/Programs/TURBOMOLE

source $TURBODIR/Config_turbo_env

export PATH=$TURBODIR/scripts:$PATH
export PATH=$TURBODIR/bin/`sysname`:$PATH

Task 3 - Copy Test Calculations from Jeremy's Directory

• Create 3 directories names test_opt, test_solv, &test_freq.

• Copy the Turbomole input files from each directory in this path /home/jerschro/UG/test_calculations/ into each directory you just created respectively.

Task 4 - Run each test calculation

• Navigate into each test calculation directory and run this command sbatch run_turbomole.sh.

Task 5 - Check to see if calculations finished correctly

• For test_opt and test_solv, see if the files converged , GEO_OPT_CONVERGED and job.last exists. This means the optimization and solvent calculation finished correctly.

• For test_freq, see if the files freq.out , vib_normal_modes and vibspectrum exists. This means the frequency calculation finished correctly.

Task 6 - Create directory structure for DNA molecules

• Create the file structure described below:
  • (You can name the DNA_molecule folder what DNA molecule you have been assigned.)

home
|
└── DNA_molecule
    |
    ├── gas
    |   |
    |   └── opt
    |   |
    |   └── solvent
    |
    └──freq

Task 7 - Install Conda

• Follow the instructions here. You need a local conda installation for next week.

Task 8 - Done!

• We will get started with the DNA molecule calculations next week. Good Work!