Energy Maps VI

Task: Run a sequence of conformations experiment to create a map of the energy search.

Time: 4 minutes

1. Use the isoprene we saved at the end of the last lesson.  If not already open, select  File|Open and navigate to the file "isoprene" you just saved.
2. Set up the experiment.
1. Select Experiment|New  
2. In the Property of: box, select conformation of a long chain.
3. In the Property box, select sequence of conformations.
4. In the Using box select standard procedure (it's MM3).  
5. Click Start. The experiment will take 30 seconds to a minute (depending on the computer).
3. The experiment status box displays the progress. CAChe stores all of the experimental results in a mechanics log file, mechanics.log. Later you may want to view this information.  
   1. Look in the isoprene.io folder for the mechanics.log file.
   2. Use a text editor or word processor to view the contents of mechanics.log.
   3. Note - you will need to choose the All Files (*.*) in the Files of type box.
4. When the experiment is completed, CAChe will display two files, side-by-side.  One is the structure of the molecule, the other is the energy map.  Before proceeding, clean up the window a little bit:
   1. Close the Experiment Status dialog box.
   2. Close the Experiment box.
   3. You may need to activate these windows (which might be hidden below the two new ones) by selecting them from the Window menu.

View the sequence of conformations in the next lesson.