Student Research

Important Things to Know

  1. Treat your research as a real class, be on time according to your schedule.
  2. Check in with Dr. Smolin or Dr. Xu when you come in and check out when you leave.
  3. Keep a detailed research log, write down all the important items from your work (detailed simulation protocols, simulation data, generated figures, movies and the path to retrieve them, and reports/presentation file locations).
  4. 15-Minute Rule: When you get stuck with a problem, spend 10 minutes trying to find a solution, then spend 5 minutes googling a solution. If none works and you are stuck for more than 15 minutes, seek help in the lab!
  5. Finish project assignments in a timely manner, think of them as homework assignments with due dates.
  6. No food/drinks in the lab. If you need to drink or eat, leave the food/drink on a stool outside the lab.
  7. Save your work or VMD visualization state before you logout.
  8. The lab desktop computers are not assigned to anyone who is not working more than half-time. You can logon any lab computers and logout when you are done. Please share the resources with other fellow researchers. Talk to me or Matt about how to keep you simulation jobs running after you logout
  9. Never power off/reset lab computers because someone else may be running jobs. If you have trouble with a computer, use another one and let Matt or me know.
  10. Lock the lab door when you leave if there is nobody else in the lab.
  11. Performance evaluation: At the end of the semester, you will present your research work. The presentation, your attendance throughout the semester, and the quality and timely completion of your research work will be used to determine the final grade, future career recommendations and scholarships.

Day One in the Lab

Here is the check list that you need complete:

  1. Obtain course permission number from Dr. Xu, if you are taking a research course (CHEM296, 396 and 495).
  2. Meet with Dr. Xu and set up a research schedule, which is posted on the group calendar.
  3. Create a research log using Google docs, name it "Firstname Lastname Semester Year Research Log" and share it with Dr. Xu and Dr. Smolin (add our emails:, and change the doc ownership to Dr. Xu).
  4. Obtain lab computer accounts from Matthew Caylor
  5. Obtain lab card key access from Dr. Xu and Donna Harryman at the chemistry dept office

Week One in the Lab

Linux Basic Commands

  1. Linux is our main research computing platform, so it's essential to be fluent with the basic commands at least. At the beginning you might find text mode command line operation unintuitive or even difficult because most people are used to Windows or Mac. However, once you spend a bit more time with Linux, you will see how powerful it is to use command lines. Watch this video to get yourself started. We have a Linux command cheat sheet poster in the lab. If you need help, ask anyone in the lab at any time. Matt is our sysadmin and Linux guru. Google search and youtube can also be very useful.
  1. Right click your desktop and open a terminal window, run
    1. cp ~dxu/.bashrc ~
    2. source ~/.bashrc
    3. This sets up your environment variables so that you can launch all the lab software properly.
  2. Get yourself familiar with Linux text editor "nano", just type "nano your_filename". Note that you cannot use mouse inside nano. If you prefer slow GUI editor, type "gedit filename".
  3. By the end of week one, you should know how to use the following commands:
      • ls or llt (list files and folders, llt sorts everything by time so that last modified file will appear last)
      • pwd (check where you are)
      • cd (change dir)
      • mkdir (make dir)
      • rm (remove a file or folder)
      • cp (copy)
      • mv (move)
      • cp -s (create a symbolic link instead of copying the actual file/folder)
      • ssh (secure shell remote access to all lab computers, even from home, ask Matt how)
      • scp or lcp (transfer files between computers, say savor and allspice)
      • nano (or gedit)
      • evince (open pdf files)
      • nohup (no hangup, keep your jobs running even after you logout)
  4. You will be quizzed on these basic commands frequently.

Molecular Visualization

  1. VMD (Visual Molecular Dynamics) is the most popular molecular visualization program, it is used to make most of the stunning figures and movies in our research. You will spend the first week going over 3 VMD tutorials. VMD has been installed in the lab. It's free, so you are encouraged to download and install it on your laptop or home computer from here
  2. The 3 tutorials you need to go over are VMD Molecular Graphics (Using VMD), VMD Images and Movies Tutorial, (the tutorial files are available at UIUC) and Using VMD with AMBER. Make sure to follow the online HTML version of the tutorials, the pdf version is reportedly missing some sections.
  3. Matthew and Dr. Smolin can show you how to download and set up the tutorial files in the lab.
  4. You are also encouraged to explore the tutorials for 2 other very popular molecular graphics program, they are also installed in the lab.
    1. Chimera Chimera tutorials
    2. Pymol Pymol Tutorial1 Pymol User Manual

At the end of the first week, you will be able to show off the pretty figures and movies you created from the tutorials, and you will be given a new molecule to apply the visualization techniques and create different representations and movies of the molecule. Here is an excellent example of VMD movie made by Andy Coombs.

Week Two in the Lab, Project Specific Training