HW1

2017

Due 01/20/2017

Submit to jqian@caltech.edu

Part 0:

A note on notation: Things in italics will be literal commands that you type into the terminal. These will
usually be preceded by a percent sign to indicate this is a terminal. DO NOT TYPE IN THE PERCENT
SIGNS. Angle brackets denote general variables that you should replace with the correct value. DO NOT
INCLUDE THE ANGLE BRACKETS. For instance, <username> for me would mean jqian. So,

% ssh <username>@atom.wag.caltech.edu

means I should type in ssh jqian@atom.wag.caltech.edu into a terminal.

If you use Windows and have not already done so, you'll need to install mobaxterm, which is available
at: http://mobaxterm.mobatek.net/. For Mac user, no need to download mobaxterm, and open
terminal directly.

In this problem set we will use a quantum mechanics/density functional theory code called Jaguar to
optimize the structure and compute vibrational frequencies and MOs of butadiene. A program called
Maestro provides a graphical user interface for preparing Jaguar input files. We’ll be using for the first
two problem sets. Download it from: http://www.schrodinger.com/freemaestro/

Part 1: Maestro

1. Download and start Maestro on your laptop (recommended)

Or

1.1 You may also be able to run Maestro from the terminal by SSH’ing into a workstation using the

following commands:

ssh –Y “node-1-4”

maestro

Or

1.2 Edit the .cshrc file using the command:

vi ~/.cshrc

Then, add the following line to the end of the .cshrc file. Press i to enter insert mode and press esc to
exit insert mode.

setenv LM_LICENSE_FILE @10.254.1.1

Then, save and quit

:wq
Now, every time you'd like to run maestro, log onto our group's fast Fermion node:

ssh -Y fermion@wag.caltech.edu

Then, log onto one of the group's Fermion nodes

ssh -Y node-4-1

...

ssh -Y node 4-5

And then, run maestro using the following command

/exec/schrodinger_2016_3/maestro

After a short loading time, a maestro window should pop up. (**If all the methods above failed, see TA
at office hour Thursday 5:00pm.)

If your Maestro looks like this, read on:

2. Create a project entry for the butadiene. (Right click -> create project entry)
3. Build a butadiene molecule using Maestro using the various building tools available from the
GUI.
 4. Go to Applications → Jaguar → Optimization. We will use the chemist's darling DFT: B3LYP with
the 6-31G** basis set. Choose these in the Molecule and Theory tabs. In the Properties tab,
select Vibrational Frequencies.
5. Copy Jaguar input file to clipboard. To view the Jaguar input file, go to input tab. In the drop
down menu next to “Job name:” select “edit.” Part 2: Running Jaguar

If your maestro is the newest version, read this:

2. Build => Create new entry => Rename it as butadiene (see read boxes)
3. Draw (pencil sign) => draw butadiene (put your mouse at the previous hydrogen and click
allows you to connect C2 to C1; put your mouse at the bond and click allows you to change
single bond to double bond)
4. Task (green box) => Jaguar => Optimization, We will use the chemist's darling DFT: B3LYP
with the 6-31G** basis set. Choose these in the Molecule and Theory tabs. In the Properties tab,
select Vibrational Frequencies.
5. Copy Jaguar input file to clipboard. In the drop down menu next to “Job name:” , click this

sign , select “edit.” Copy the input file into a clipboard.

Part 2: Linux terminal

1. For Windows users, start mobaxterm. If you use a Mac, you should be able to simply open a terminal
and type

% ssh -Y <username>@atom.wag.caltech.edu

I recommend creating a new directory for each problem set via

% mkdir HW1
and entering that directory via

% cd HW1

2. Now, create transfer the input file created by maestro into this directory.

% vi butadiene.in

Once in vi, enter insert mode by pressing “I”

Paste your jaguar input file

In vi, use “esc” to exit insert mode

Exit using “:wq”

3. Now submit the job to the cluster

Copy jaguar job submission python script qsubjaguar.py by

% cp ~jmendoza/bin/qsubjaguar.py .

(here . means keep the file name)

NOTE: you need to change the LICENSE number in qsubjaguar.py, just like what we did previously to
@10.254.1.1

submit the job now

% qsubjaguar.py butadiene.in

(You can check on your job status and get the PID with % qstat -u <username>

You kill a job by % qdel <PID>)

5. After optimization, you should see three more files: <fname>.out, <fname>.log and <fname>.01.in at
the same directory. (Be sure to check if your .out file has coordinates and minimization data before next
steps!) We can visualize the optimization process by converting the .out file to .xyz file to see how it
converges to the stable structure. Use the script

% jaguar babel -ijagout <fname>.out -oxyz <fname>.xyz

to get the xyz file. Then type

% /source/molden/linux/molden4.2.linux <fname>.xyz

to view the trajectory of optimization. Click “movie” to show the trajectory, click the skull button to quit.

6. Use the script

% /ul/wgliu/bin/jaguar/molfreq.py <fname>.out > <fname>.freq.molf

To generate frequency files for molden, and you can use molden:
% /source/molden/linux/molden4.2.linux

to visualize all vibrational modes. Click the “Norm. Mode” box to show the modes.

(you need to load the .freq.molf file from last step by choosing it in “READ” box)

Part 3:

7. In Maestro, open <fname>.01.in, which contains the geometry of the optimized molecule and the
wavefunction. Now we want to plot MOs of this molecule. To generate new orbital files from optimized
structures, we calculate single point energy (Note, all Quantum Mechanics calculations in maestro is
under jaguar, in 2016 version should be task -> jaguar-> single point energy), check the surface box in
Properties, and select MO from HOMO-1 to LUMO +1 (MO 14-17 in the molecular orbital list). (EXTRA
POINT +1: explain what is α, β HOMO and LUMO selection, and why we need to select both? HINT:
Maestro User Manual) Also check the Mulliken population’s box. (EXTRA POINT +1: report the
difference in method: atom, atom and basis function, bond population) After the job is done, you should
see four “.vis” file in the same directory. Go to Display->surfaces->import to load .vis file. Choose “entry
from all” and check the geometry we want to put MOs on. You need to look into the output file and find
the mulliken charges. Refer to the next step for how to use text editor vi.

8. With the same <fname>.01.in, we are now going to investigate the energetics of rotating butadiene
about the C2 – C3 bond in C1 = C2 – C3 = C4 (the C atoms may be indexed by other numbers). Ensure
that the optimized butadiene molecule is selected and from the Jaguar menu option, select Relaxed
Coordinate Scan. The new window should be familiar, as it’s exactly the same as the Optimization
window with one important change: there is now a Scan tab. Click on this tab and select Dihedral as the
type of constraint in the ‘add new coordinate’ box. You will now select the atoms involved in the
dihedral that you want to rotate about, so sequentially select the 4 carbon atoms in the following order
C1 C2 C3 C4 and the dihedral angle will show up in the ‘defined coordinates’ list. In the Selected
coordinate box, enter 180 as the starting value, 360 as the final value and 20 as the increment. This
should give you 10 scan points. Write out the input file (you may want to change the input file name to

<fname>_scan.in) and submit to atom using

% qsubjaguar.py <fname>_scan.in

Once finished, search for the keyword “scan”, and you will get the energies of each increment of the
angle. Note: You can use text editors like vi, emacs or gedit to view the input and output files. Take vi for
example, use “vi text_<fname>” to view the file, use j, k, h, l, PgUp, PgDn or the arrow keys to move the
icon. Type “:q” to quit. For more: http://www.imss.caltech.edu/node/324#f_editors

Use the following command to search for the lines that contains energy information in your output file:
grep –in “scan.*energy” butadiene_scan.in

For more about searching through files: http://www.imss.caltech.edu/node/324#f_searching

To see what the scan looks like, we can convert the .out file to .xyz file by using jaguar babel. You can
also get the .xyz file for the overall potential surface by

% perl ~wgliu/bin/stepin2xyz.perl
You should be prompted to enter <fname>.steps.in, and you will get the converted <fname>.xyz file.
Open the .xyz file in molden, click “movie” to show the scan, click the hourglass button to slow down the
movie. Click “Geom. conv.” to show the potential energy curve.

Write-up:

1. Report the geometries (bond length and bond angle), Mulliken charges and energy of the ground
state of butadiene (cis or trans?). Report the vibrational frequencies and identify the characteristic
vibrational frequencies by C-H and C-C. Look up experimental data (geometry and vibrational
frequencies) from NIST database: http://webbook.nist.gov/cgi/cbook.cgi?ID=C106990 and make a
comparison.

Note: In maestro, use tools->measurement to get the bond lengths and angles. You may need to explore
the above link to get the experimental data.

2. Report the rotational barrier and energies in kcal/mol. Is the geometry at dihedral angle 0 a local
minimum? Explain your result.

3. Plot HOMO-1, HOMO, LUMO and LUMO+1 of the ground state of butadiene (in maestro, use maestro
--> save image).

Either email the write-up to jqian@wag.caltech.edu or turn it during class on Friday