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Gomez Research Group
Department of Chemistry, Mount Holyoke College


First Semester

Course Home

First Research Semester

On your first research semester, you would get familiar with your system, typical program tools used for your system, and learn how to program in C++. The latter will allow you to create program tools that have not been made before. All new research students would meet together with me to go over the pieces learned each week. After the first semester, you would have meetings with the team associated with your specific system. The time commitment for learning these new ideas and skills is roughly 8 hours of work on the projects and a one hour meeting with me and the group of new researchers. As with a standard class, it will take different people different amounts of time to get projects done so this is a very rough idea. You need to sign up for four credits of independent study for this introductory semester. After that you may sign up for research in 2-6 credit intervals with each two credits being approximately 4 hours of research. All research indepdent studies will have the grading structure specified in the syllabus. The mid-term and final papers on the first semester would summarize and give results for the introductory projects listed below.

  • Learn how to use a linux system (week 1)
    • Introduction to Linux is a good general reference.
    • Quick guide to basic commands you'll use is found on Evernote under Useful Commands. Feel free to add new commands you find useful there. Use these to login into medusa, list your files, make a directory, make a file (emacs or vi), move a file from one directory to another, copy the sample files from my directory to yours, transfers files from a mac to medusa and back. Also other useful linux sites are on Evernote under Useful Sites.
  • Make a picture of your system and outline research project (week 2)
  • Find some minimum energy structures for your system and one transition state. (week 3, 4)
  • Learn some programming basics (week 5, 6)
  • Monte Carlo (week 7, 8)
    • Frenkel and Smit, Understanding Molecular Simulation, Chapter 3 (Book is in the lab.)
    • Explore the sample Monte Carlo program
    • With the harmonic oscillator model, verify that you get the right energy
    • Find out how long an equilibration is long enough and how large a sample size is needed to get convergence in the average potential energy. Experiment with the parameters and see how changing them effects convergence.
    • Extra notes on program and answer key to check results with is on the group wiki page under Monte Carlo Tutorial in Project Menu.
  • Simulated Annealing (week 9, 10)
    • Convert the Monte Carlo code to a simulated annealing code
    • Change the potential to a potential with multiple minima
    • Verify that your simulated annealing code works
    • Come up with ideas on an optimum schedule for annealing
    • Extra notes on program and a useful reference are on the group wiki page under Monte Carlo Tutorial in Project Menu.
  • New Project Program (week 11, 12)
    • During this week you'll read through current research proposals to see which project is the best fit for you. We'll make an outline of the project and then start on it. You'll continue on this project in the summer and/or in future semesters.

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This page created and maintained by Maria A. Gomez ( Last modified on November 19, 2011.