Stretching Deca-Alanine: Setup

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Setup

Since the system is small (104 atoms), you will be running all simulations and calculations on local machines.

You will make a copy of the files needed for these exercises in a directory called tbss.work in your home directory. In a terminal window, move to this directory by typing:

tbss> cd ~/tbss.work

Copy the needed directory, but instead of typing TOP_DIR, type the location of the Summer School directory tree:

tbss> cp -rp TOP_DIR/sumschool03/tutorials/03-10Ala_tutorial/files ./10Ala_tutorial

For instance, if the materials are located at /mnt/cdrom or at ~/Desktop, replace TOP_DIR by /mnt/cdrom or ~/Desktop. Use this copy of the tutorial files. Change your current directory to 10Ala_tutorial by typing

tbss> cd ~/tbss.work/10Ala_tutorial

Next: IMD simulation Up: Stretching Deca-Alanine Previous: Introduction