[CHM Research] A different approach

[Andrew Pounds]

Ann and Shannon -- please forgive my lack of communication.  We've had a 
lot going on with the final week of school and softball.  My daughter 
Natalie's team one the championship tournament last night. Because it 
was a double elimination tournament we had to win three games back to back.

Anyway, while I do want you two to experiment more with Molden, I also 
want to get you started using Molden in tandem with Gaussian to minimize 
and examine structures.  This is a multistep process where you build a 
molecule in Molden, save it, insert commands for Gaussian, build a 
script for the batch scheduler, run the job, examine the results, and 
repeat as needed.

I am actually trying to make a "manual" that walks you through this 
process, but you two are also my "experimental subjects" to see if my 
instructions can be turned into results.

If you are ready to dive in, here is what I want you to do.

 1. Create a directory called tppwork and change into it
 2. Once you are inside the tppwork directory, get into Molden and build
    triphenlyphosphine in the following manner
     1. Add a fluorine atom and then add a carbon atom that is attached
        to the fluorine
     2. click on the carbon atom that you just added and replace it with
        a methyl fragment
     3. after you do this you will probably have to run the tinker
        "optimize" feature to get everything into a nice tetrahedral
        structure.
     4. after optimizing with Tinker, replace each of the methl
        hydrogens with a phenyl group
     5. click on the central carbon and change it to a phosphorous in
        the Z-matrix editor
     6. click on the fluorine and change it to an "X" -- which is a
        dummy atom that is only used to help build Z-matrices and
        specicy symmetry points.  Be sure to hit the button to apply the
        changes to the current Z-matrix.
 3. You should now have a triphenylphosphine molecule on the screen with
    the phenyl groups all aligned with the C3 molecular rotation axis. 
    Click on the "Gaussian" button at the bottom of the screen and then
    click on the "Submit Job" button.  Once the new dialog box opens up
    do the following:
     1. Set the basis set to 6-31G*
     2. click on the "Batch" button.  If you don't do this Molden will
        just start running a gaussian calculation and you won't have any
        control over it.  Since molden does not automatically reload the
        results of a completed Gaussian calculation, this make no sense
        (we'll handle that in a minute)
     3. Click "Submit".  You will get a notification that the job has
        started -- but it really hasn't.
     4. The Gaussian input file (which we need to modify) should now be
        stored in a file called test.com.  You may exit out of Molden.
 4. Copy the test.com file to a file named "tppstart_opt.com"  using the
    "cp" command
 5. Open the tppstart_opt.com file in your favorite editor.  A the top
    of the file you will see a line with the $ RunGauss command.  Delete
    this entire line.  After the keyword "Opt" insert a space and add
    the keyword "freq".  Change the title to something you like.  Save
    you changes and exit the editor.
 6. Now we are going to create a job file for the batch scheduling
    system.   Use your editor to create a new file.  You will probably
    use something like "evim tpp.pbs" or "gedit.pbs".  Add the following
    lines to the file:

        #PBS -N TPP_TEST
        #PBS -m abe
        #PBS -j oe
        #PBS -l nodes=1:zeus:ppn=1,walltime=24:00:00
        #PBS -M pounds at theochem.mercer.edu
        #
        source $g09root/g09/bsd/g09.profile
        cd $HOME/tppwork
        g09 tppstart_opt

Then exit the editor.   In order this file (1) sets the name of the job 
(2) tells the batch system to mail you if the job aborts, ends normally, 
or crashes (3) joins the output and the error files from the job 
processing system into one file  (4) sets the number and name of the 
node on which to run the job, the number of processors to schedule on 
that node, and the amount of time to allow for the job.  I have that set 
at 24 hours.   The final setup command defines the e-mail address to be 
notified when the job completes.  PLEASE CHANGE THIS TO YOUR EMAIL.  
After that are the commands to ensure that your Gaussian environment 
variables are all defined properly, change to the directory where your 
files are located, and then to run Gaussian on the file you just created.

 7. Once you have this file created type "qsub tpp.pbs".   You can then
    monitor the status of your job using the qstat and showq commands. 
    This job should run in less than two hours.  It could take longer
    based on system load.  You do not have to stay logged on while the
    job runs.
 8. After the job completes, get back into the tppwork directory and
    open the file tppstart_opt.log. Look for the first occurrence of the
    word "Frequencies" in the file and send me the number that appears
    immediately after that word on the same line.






-- 
Andrew J. Pounds, Ph.D.  (pounds_aj at mercer.edu)
Professor of Chemistry and Computer Science
Mercer University,  Macon, GA 31207   (478) 301-5627
http://faculty.mercer.edu/pounds_aj

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