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<font face="serif">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. <br>
<br>
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. <br>
<br>
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.<br>
<br>
If you are ready to dive in, here is what I want you to do.<br>
<br>
</font>
<ol>
<li><font face="serif">Create a directory called tppwork and
change into it</font></li>
<li><font face="serif">Once you are inside the tppwork directory,
get into Molden and build triphenlyphosphine in the following
manner</font></li>
<ol type="a">
<li><font face="serif">Add a fluorine atom and then add a carbon
atom that is attached to the fluorine</font></li>
<li><font face="serif">click on the carbon atom that you just
added and replace it with a methyl fragment</font></li>
<li><font face="serif">after you do this you will probably have
to run the tinker "optimize" feature to get everything into
a nice tetrahedral structure. <br>
</font></li>
<li><font face="serif">after optimizing with Tinker, replace
each of the methl hydrogens with a phenyl group</font></li>
<li><font face="serif">click on the central carbon and change it
to a phosphorous in the Z-matrix editor</font></li>
<li><font face="serif">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.<br>
</font></li>
</ol>
<li><font face="serif">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:</font></li>
<ol type="a">
<li><font face="serif">Set the basis set to 6-31G*</font></li>
<li><font face="serif">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)</font></li>
<li><font face="serif">Click "Submit". You will get a notification
that the job has started -- but it really hasn't. <br>
</font></li>
<li><font face="serif">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.</font></li>
</ol>
<li><font face="serif">Copy the test.com file to a file named
"tppstart_opt.com" using the "cp" command</font></li>
<li><font face="serif">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.</font></li>
<li><font face="serif">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:</font></li>
</ol>
<blockquote>
<blockquote><font face="Courier New, Courier, monospace">#PBS -N
TPP_TEST </font><br>
<font face="Courier New, Courier, monospace">#PBS -m abe</font><br>
<font face="Courier New, Courier, monospace">#PBS -j oe</font><br>
<font face="Courier New, Courier, monospace">#PBS -l
nodes=1:zeus:ppn=1,walltime=24:00:00<br>
#PBS -M <a class="moz-txt-link-abbreviated" href="mailto:pounds@theochem.mercer.edu">pounds@theochem.mercer.edu</a><br>
</font><font face="Courier New, Courier, monospace">#</font><br>
<font face="Courier New, Courier, monospace">source
$g09root/g09/bsd/g09.profile</font><br>
<font face="Courier New, Courier, monospace">cd $HOME/tppwork</font><br>
<font face="Courier New, Courier, monospace">g09 tppstart_opt</font><br>
</blockquote>
</blockquote>
<font face="serif">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. <br>
<br>
</font>
<ol start="7">
<li>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.<br>
</li>
<li>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.<br>
</li>
</ol>
<font face="serif"><br>
<br>
<br>
</font><font face="serif"><br>
</font><br>
<pre class="moz-signature" cols="72">--
Andrew J. Pounds, Ph.D. (<a class="moz-txt-link-abbreviated" href="mailto:pounds_aj@mercer.edu">pounds_aj@mercer.edu</a>)
Professor of Chemistry and Computer Science
Mercer University, Macon, GA 31207 (478) 301-5627
<a class="moz-txt-link-freetext" href="http://faculty.mercer.edu/pounds_aj">http://faculty.mercer.edu/pounds_aj</a>
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