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NewStudentTasks

To come up to speed on the simulations that we do in this group, please complete the following steps.

Obtain an account on the BYU Super Computer
1. Navigate to https://rc.byu.edu/
2. Click on "Request and Account" link in the upper right-hand corner of the webpage.
3. As part of the application, you will need to write short description on why you need supercomputing resources. This should be something like the following.
I am going to do research with Dr. Knotts in chemical engineering. I will be running molecular dynamics and monte carlo simulations of biological molecules to study molecular-level interactions and behaviors. These are very computationally-demanding computations that require dozens of processors running for weeks at a time. My main area of study concerns the behavior of proteins on surfaces. I am trying to determine how different types of surfaces affect the stability of tethered proteins with the ultimate goal of creating medical diagnostics and defense-capable sensors.
See Dr. Knotts and get an account on watt.et.byu.edu (our group server). (You can continue with the steps below before completing this step if needed.)
Learn basic bash/linux commands
1. cd, cp, mv, rm, ssh, scp, etc.
2. Search the web for "basic linux commands"
3. Visit the supercomputers introduction at https://rc.byu.edu/documentation/unix-tutorial/
4. Visit Basic Bash Commands
Practice creating/editing files with the VIM Editor
1. VIM is an powerful editor of text files that will be found on every linux machine.
2. Google "VIM editor tutorial"
Start learning how to program in C and C++.
1. Google “C tutorials” to get started.
2. Program a simple “Hello World” application
3. Submit it to the super computer for practice.
  1. There are examples of submission scripts on the supercomputer website and here.
  2. You will have to compile your code. Search for “compile code with gcc” on the web.
Learn the basics about Molecular Dynamics and Monte Carlo simulations.
1. Professor David Kofke has a good overview that can be found here.
  1. Visit the link “Lectures” where many of the basics are explained.
2. You can also search “Molecular Dynamics Simulations” and “Monte Carlo simulations” on Google.
Practice compiling code, submitting to the supercomputer, and interpreting results using a Lennard Jones Fluid
1. Download the Lennard Jones (LJ) simulation code (zipped in two different formats) below.
  1. ljmdmc.zip (Windows or Linux)
  2. ljmdmc.tar.gz (Linux)
  3. See README and ljmdmc-doc.pdf located in the doc folder for help compiling and running the program.
2. Compile the code and submit several simulations to the supercomputer to reproduce the standard results for a LJ fluid.
  1. The NIST standards can be found here.
  2. Create plot to explain how well you can reproduce the data. Make sure to do replicates.
  3. You will need to do several simulations at different temperatures/densities and using MD/MC to reproduce the data.
  4. You don't have to reproduce everything that NIST does, but you want to do enough to feel comfortable with compiling, submitting, and data gathering.
Learn about your system of interest (Google)
1. Learn the basic biochemisitry of DNA and proteins.
  1. For proteins, you want to understand protein synthesis and protein structure
  2. For DNA, you want to understand structure and hybridization.
2. Learn about protein arrays and DNA microarrays.
Once you get this far, contact Dr. Knotts and you can start running some simulations.