Homework 2

Ch121a, Due Friday, Feb 3 2017
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1Introduction

In this assignment we are going to carry out additional density functional theory calculations using Jaguar and the maestro visualization software.
Density functional theory (QM) calculations are remarkably accurate, but are too expensive to run for systems larger than a few hundred atoms. For these large systems, classical force-fields trained to reproduce QM energies are useful. Today, we are going to motivate the use of force fields and begin training an H2O force field.

2H2O calculations

Let’s start by doing some calculations on water.

In order to run Maestro, you need to load the appropriate license file (which you probably did for homework 1). If you haven’t already, add the following line to your .cshrc file.

setenv LM_LICENSE_FILE @10.254.1.1

First, we will load maestro. For the purposes of speed, I recommend logging onto an ion node.

ssh –Y

The –Y enables X11 forwarding, which enables the Maestro window to load. The above command will log you onto the ion front end. The front end can become crowded if too many people use it at once. I recommend logging onto an ion compute node using one of the following commands.

ssh –Y node-1-5

ssh –Y node-1-6

ssh –Y node-1-7

ssh –Y node-2-3

ssh –Y node-2-4

ssh –Y node-2-6

ssh –Y node-2-7

ssh –Y node-2-8

Once you are logged onto an ion compute node, create a folder for your homework 2 file, i.e:

mkdir homework2

cd homework2

Then, load maestro using the following command

/exec/schrodinger_2016_3/maestro

The Maestro window will load. Start a new project using Project->New Project. This project will contain all information related to homework 2.

Now, let’s construct our H2O molecule. Note that these instructions refer to the “Original” Maestro view. Some buttons may have moved in the new version.

Go to the fragments toolbar and add an H2O molecule. Alternatively, construct an H2O molecule from the build toolbar

From the build toolbar, press “clean up geometry” to minimize

Now, let’s set up a geometry scan.

Go to tasks->quantum mechanics->rigid coordinate scan.

OR applications->Jaguar->rigid coordinate scan

Change the jobname at the bottom of the window to something reasonable (ie h2o_scan).

Enter the scan tab on the window. Select “Distance” and “Pick: atoms” in the add new coordinate section of the window. Then, click on the O atom, followed by the H atom. The last atom you click will be the one that moves.

Then, adjust the O-H bond length from .8 angstroms to 3.0 angstroms in intervals of .2 using the selected coordinate interface on the right of the screen.

Click the gear in the bottom right of the window and set the host to “Atom”, which generally has processors available for quick jobs. To speed up the calculation, increase the number of CPUs used to 4. Then, press run. When the job is complete, a new entry will appear in the project table on the left hand side of the main Maestro window.

If you prefer submitting jobs from command line, you can access the jaguar input file from the dropdown menu next to the gear. These input files can be submitted using the following script/ul/brooks/bin/qsubjaguar.py FILENAME.

While the job is running, let’s look at the input and output files produced by the previous calculation. Open a new terminal window and head into the job directory.

(Open new terminal window)

cd homework2

ls –l

cd JOBNAME

ls -l

Take a look at the output files. Briefly describe which each one does (or looks like it does). If you need an additional reference take a look at the “Jaguar User’s Manual.” It is easily accessible via google.

Now, the final energy is labeled “SCFE” in the jaguar .out files. You can list these energies using the command:

grep SCFE *.out

You may also find the .grd file useful for obtaining a list of final energies.

Now, plot energy as a function of bond length using your preferred plotting software. Does the behavior look like a Lennard-Jones potential?

Now, let’s adjust the H2O bond angle. Go to edit->adjust->angle and run calculations for 4 different angles. Plot energy as a function of angle (HINT: you may have to look through the .out produced by jaguar)
OPTIONAL: Create a system of two H2O’s. Use the adjust tool to line an H’s from the first H2O with the O from the second H2O. Then, adjust the distance between the using applications->quantum mechanics->relaxed coordinate scan. Plot energy as a function of H2O-H2O distance. What is the shape of this curve?
Now, create systems of 1, 5, 10, 15, and 20 H2O molecules. Run a single point calculation (applications->quantum mechanics->single point energy) for each case. Plot computation time as a function of number of atoms. Suppose you had an hour to perform a calculation, about how many atoms could you include. What if you had a week?

In class, Bill mentioned terms included in various force-fields. What terms do stretching a bond, changing bond angle, and changing H2O-H2O distance correspond to, in say, the AMBER force field?

Reference on AMBER:

In summary, you’ve analyzed quantum-level calculations of water and derived energy descriptions that can be used to train classical force fields. Later in the course, you will use a force fields to run large-scale simulations of water molecules impacting a surface.